The Wizard's Handbook Part I

Attributes, Races and Class Features

Wizards are a vast class. Two wizards may differ in so many areas, even if their builds are similar. The main reason for that is of course, spell selection. Just by looking at the wizard 'shell', you can tell that they're lacking in many areas: bad base attack bonus, only one good saving throw, low skill points and just a few feats as their special features over 20 levels. So what is it that makes them so special? Yup, you guessed it: spells.


The Wizard's Handbook Part I: Attributes, Races and Class Features
The Wizard's Handbook Part II: Skills and Feats

Attributes

Strength: This is a dump stat for wizards. It only applies to melee touch attacks, but since they are touch anyway, you won't have much of a problem with this. Note that strength is the only one of the attributes (casting aside) that benefits a character for having an odd score.
Dexterity: Not a dump stat, but not primary either. Try to keep this as high as you can, without hurting your constitution and intelligence. A high enough dexterity will optimize your ranged touch attack modifier, so that you can successfully target all enemies with your rays (some of the most powerful spells require ranged touch attacks, such as the potent debuff Enervation). In addition, it will provide a minor boost to your initiate and reflex saves. Reflex saves might not be that important, but a high enough initiative rating greatly helps and every little bit counts towards acting first in the combat sequence, making you able to cast an important buff or debuff (Haste, Summon Monster, Wall of X, etc).
Constitution: This needs to be really high. A close second to intelligence, constitution boosts your fortitude saves and your hit points. Wizards lack in both areas, which are arguably the most important aspects of a character. Remember that to be useful to a party you need to cast spells and you can't cast them when you're dead. A minor note is that it also boosts your familiar's hit point total, too. Also the concentration skill, which all wizards should max out, is keyed off constitution.
Intelligence: This is your primary statistic and should always be as high as you can, which means that you should sink items that provide bonuses to attribute scores (like Headband of Intellect) and your bonus attribute points from levels. Determines your save DCs and bonus spells. Also many of the wizard's skills are keyed off intelligence (Knowledges, Crafts, Decipher Script and Spellcraft) and you're receiving bonus skills points for having a high score. Starting wizards require a 15 minimum score in this attribute in order to acquire 9th level spells in time (by using the bonus attribute points in intelligence).
Wisdom: Normally wisdom is a statistic you can dump. Only helps will saves, which are already high.  The feats or requirements you'll want to fulfill will rarely require a wisdom score that is higher than a 10 (just to avoid the penalty to will saves), with one noteable exception: the feat Arcane Disciple, which adds the spells from a single cleric domain to your spell list, a very potent way of expanding your spell selection, requires you to have a wisdom score of 10 + the spell level, which means that to max out the feat's effectiveness you need a wisdom score of 19.
Charisma: Dump stat, but there are exceptions. A significant number of spells require you to make charisma checks or to win on opposed charisma checks (Command Undead, Planar Binding).

Races

Not all races are suitable for wizards. This are some points to take into consideration hen choosing a race for your wizard:

Feats: While wizards receive a fair amount of bonus feats, most builds are feat
intensive. Also if you are going to prestige, your feat selection will be a lot more strict. For example consider an archmage, a usual choice as a prestige for wizards, which requires 3 feats that aren't exactly helpful. So if your new class doesn't provide bonus feats, consider selecting a race that helps (a prime example is the human race).
Attributes: Be extremely careful here. Choose races that don't give penalties to your key attributes: intelligence and constitution. A wizard can survive a hit in nearly every other attribute, but not make the mistake of reducing those two, because you may regret it, even from the start of the campaign. On the other side, when looking for races that provide bonuses to your attributes, choose those that boost constitution and intelligence. Bonuses to dexterity are always nice and wizards can benefit from some charisma. A common choice for the wizard class are elves (especially high elves, that boost intelligence and dexterity, but receive a hit in strength and constitution), but unless you know what you're doing (e.g. need to fulfill a prestige class requirement) don't pick them as your race, or at least do anything you can to avoid the constitution hit.
Type: This is important to wizards more than one may think. This is because of two powerful spells, alter self and polymorph. Not the first priority, but types other than humanoid (such as construct, dragon or outsider) are welcome.
Level Adjustment: Even if these races seem attractive, don't ever, ever take level adjustment beyond one or two points and that's the case only if you are allowed to buy it off. Wizards are powerful because of their spells. If they don't have access or get late access to them, it won't make you happy. The penalties will be vast late game and because you actually will be very fragile , early in the campaign you will be a nuisance and viability to your team. Taking level adjustment will make you lose BAB, skills, spellcasting and saves.
Skills: Not important to wizards. Bonuses to skills are respected, but don't choose races based on that. You'll already have a nice amount of skills per level from your main casting stat, more than enough to cover your needs.
Favored Class: There are many races that list wizard as their favored class. Don't let that fool you. A race with favored class (wizard) means that traditionally, members of this race are involved with the certain class. However that doesn't actually mean that they are good for it. For example, elves as presented in the PHB are a bad option for wizards.
Size: A small wizard is actually better in several aspects from medium ones. Being small gets you a mild AC and attack bonus, which is great for touch attacks. Also they receive some bonus to the hide skill and generally small races receive bonuses to move silently, too. However, note, that you become more vulnerable to grapple/pin attempts, trip attacks, disarm bull rush, overrun attempts and your speed generally is lower than that of medium sized default speed (30ft).
Languages: You are going to have a whole lot starting languages. Standard wizard languages are elven and draconic, as a lot of arcane-related texts are written in these. Choose carefuly the rest and make sure that you and your party share a common obscure language if you need to communicate without others understanding.
Movement Modes: Speed is not all that important to wizards, because they do have speed boosters or spells that allow tactical movement. So it shouldn't matter a lot in your selection. However alternate movement modes are respected, such as a climb or fly speed, especially at low levels. Never get a particular race for the bonus alternative modes though. They are easily duplicated with low level spells.
Weapon Proficiencies: Wizards have a very strict selection of weapon proficiencies. Races that expand this are welcome, but shouldn't be the main reason you chose it. Weapon proficiencies are not above attributes for example. Choose wisely.

This is a list with most of the no or low level adjustment races that are often used for wizards. Also here is a nice little guide by AZNsupermarket that was unfortunately archived.

Humans ^PHB: Bonus feat, skill points and any favored class. As with everything else, humans make for very good wizards. If you are a new wizard player and you are not sure about your race selection, you can never-ever go wrong with picking the human race.
Dwarfs ^PHB: Not the best wizards out there, but this race does boost your defensive skills. Especially nice is the stability and constitution bonus. Also darkvision and the other various abilities are respected.  Dream Dwarfs switch the penalty to dexterity can hurt certain builds, but the tradeoff is ok. This gets the standard dwarf bonuses (stability, constitution bonus) but also possess the Dream Sight ability, which is not that great, and spell power with divination spells and earth descriptor spells, only when in contact with the ground. All of these bonuses come at no level adjustment. 
Elves ^PHB: Elves as presented in the player's handbook are a viability to wizards. The only real bonus is the weapon proficiencies, for which you shouldn't really care about. Constitution loss is a pain, considering that you will start with 5 or so hit points. However, it must be noted that elves have access to elf paragon ^UA which boosts your intelligence by +2. Since most elves gain weapon proficiencies, are able to qualify eventually for the abjurant champion ^CM prestige class at the expense of just a feat. Gray Elves are just a little better, since they offer a bonus to intelligence; they are a nice choice if you apply the dragonborn template to them, making their racial attribute modifiers -2 strength +2 intelligence. The Artic and Desert elf varieties (from Unearthed Arcana) switch the penalty from constitution to strength: not the best, but can be used if you desperately need to be an elf for a prestige class. Another option from the same book is Fire elves (you can also make them dragonborn) for racial stat modifiers of +2 intelligence -2 charisma. Making them dragonborn also removes the penalties and bonuses for being of fire heritage. The Sun Elves from Forgotten Realms Campaign Setting have a bonus to intelligence, but penalty to constitution. This is a common choice for wizards, and while it is better than the PHB elves, the constitution penalty hurts. I wouldn't recommend these at all. There are so many ways to raise your difficulty class and gain extra spells, that at higher levels, the intelligence bonus won't even matter. A nice thought is again using dragonborn ^RotD so that you move the constitution penalty to your dexterity, while retaining your intelligence bonus. The elven benefits are not that great to wizards and you are still considered an elf for various effects.
Gnomes ^PHB: Bonus to constitution and spell power with illusion spells. Small size and even some spell-like abilities. Gnomes generally make good wizards, but you should also take a look at the various gnome subraces in sourcebooks (especially Chaos gnomes and Whisper gnomes). In addition a (hidden) gem in Monster Manual I are Forest gnomes, which have the standard gnome bonuses in addition to Pass Without Trace at will and a simple language that enables them to communicate with forest animals (albeit at a very basic level). Being a gnome makes you eligible for one of the top wizard prestige classes, the Shadowcraft Mage. Chaos gnomes (from Races of Stone) are a good alternative if you are allowed to use level adjustment buyoff .The attribute bonuses are great, to nearly every stat you'll need in your career. It has some nice bonuses, including the thematically synergistic spell power and luck of chaos. Another great gnome subrace are Whisper Gnomes (from Races of Stone). The attributes are ok (the charisma loss might be problematic, but most of the times won't), base land is 30ft even though they are small and receives huge bonuses to move silently/hide checks, making them ideal for sneaky wizard builds (Unseen Seer ^CM, Arcane Trickster ^DMG).
Halflings ^PHB: Small size, bonus to dexterity and some great saving throw bonuses. The sourcebook Forgotten Realms Campaign Setting had two halfling varieties: Strongheart Halflings that receive a bonus feat like humans instead of the +1 to saves. This rivals humans ^PHB for the best wizard race, because  of the small size. Ghostwise Halflings have the ability to communicate telepathically, which is a great way for enchanters to give orders to their minions. Again they retain all the standard halfling bonuses, but lose the +1 bonus to all saves.
Illumians ^RoD: The illumian race favors basicaly multiclass characters. The obvious reason to get this race is for the sigils it offers. The best luminous sigils for wizards are probably Naen and Krau. Krau is only useful in the case you acquire a prestige class that sacrifices one or two levels from your casting progression. That way you get back you lost caster levels, without having to spend feats on practiced spellcaster ^CA for example. Naen is pretty straightforward, as most of your skills will be keyed off intelligence. An interesting possibility is Hoon, which helps both constitution (concentration) and wisdom (listen, spot) checks and skill checks. Also they are considered human, so that may help with some feats and classes (e.g. the Able Learner feat).
Sharakim ^RoD: This receives a bonus to intelligence and a worthless bonus to strength. It hurts dexterity, which isn't that nice and charisma, which may be useful occasionally. The rest of his abilities are too crappy to deserve a +1 level adjustment, and they are easily duplicated with spells.
Tieflings ^RoD: This planetouched race features a lot of the bonuses a wizard can acquire due to his race selection. The only problem is the +1 level adjustment, but if retraining is allowed in your campaign, this problem can easily be waived. The attribute bonuses are ok, but lesser charisma may be problematic sometimes. One of the greatest bonuses of this race is its type. Outsider (native) means that even though you need to eat and sleep, you are not affected by a wide range of spells that target humanoids and that alter self and polymorph spells provide more benefits to you.  
Dragonborn of Bahamut ^RotD: Dragonborn is a template that can be added to other races. What is good about this one is that it raises your constitution, while reducing your dexterity. This is a great template, since many races that give bonuses to intelligence (such as sun elves) incur a penalty to constitution. This will help offset the differences, while getting some cool dragon features. You can select between a constitution based breath weapon (which is great feature because it doesn't require attack roll and it can be augmented by metabreath spells), sharpened senses or wings. Your type changes to humanoid (dragonborn), but it states that "For all effects related to race, a dragonborn is considered a dragon and a member of her original race".
Kobold ^RotD: What makes kobolds great wizards, despite the huge penalties in their attributes, is a single feat: Dragonwrought ^RotD. This effectively changes their type to dragon. Dragonwrought kobolds have been used to abuse various mechanics, from early epic feats acquisition to ability bonuses due to age. Since dragonwrought kobolds are true dragons, they can use great alter self forms, too.
Aventi ^Stormwrack: Aventis are amphibious humans that are haven't got anything important. They are just mentioned because of the water spell power they possess.
Amphibious Creature ^Stormwrack: The amphibious template gives you a swim speed and the ability to breathe air equally well as air. All these come only at the cost of reduced dexterity. This may prove useful to campaigns close to large bodies of water, or underwater ones. 
Lesser Planetouched ^PGtF: Located at page 191 of the book, you can choose to be a "lesser" version of a planetouched. Effectively you become humanoid with the planetouched subtype. This means that you are affected by spells that target outsiders or humanoids. Also since you are no longer an outsider, you can't take some cool alter self forms. That said, this is ok, but level adjustment buyoff is strictly better. The main advantage that tieflings ^RoD have, for example, besides some their racial attribute modifiers, is their outsider type.
Deep Imaskari ^Und: An underdark race that gives a bonus to intelligence and a penalty to dexterity. Also it has an ability that lets you recall a 1st level spell, which is great for low level characters. The description text suggests that Deep Imaskari are actually a human subrace, so they should possess the human subtype, although this is not reflected in their racial traits; this subtype will enable them to acquire human-only prestige classes or feats, like Able Learner.
Changelings ^ECS: Not actually a great race for wizards, but they open up access to powerful substitution levels and the recaster ^RoE prestige class. Do not underestimate their minor change shape ability, as it can save lives at low levels and help disguises later.
Warforged ^ECS: This is a great race for wizards. Makes you immune to lots of things, boosts your constitution and the penalties are to attributes you don't need. You also gain light fortification. One of the most important benefits of this race is that you can heal yourself with the repair damage series of spells. The downside is that you have a 5% arcane spell failure from your composite plating and that you are vulnerable to effects that target both living creatures and constructs. However since you can enhance your armor, that is not much of a problem, as you can choose magic enhancements that alleviate the arcane spell failure.

Class Features 

Wizard Features:

Low base attack bonus.
Good will save progression.
2+intelligence modifier skill points.
Proficient with the club, dagger, heavy crossbow, light crossbow and the quarterstaff.
Not proficient with any kind of armor or shield.

Summon Familiar: Familiars can be a huge boon to their masters. They are intelligent, so they can use items, essentially increasing the number of available item slots you have; they can use the aid another action to aid you (since you share skill ranks) and add +2 (or higher, if you spend some gold to get some items) to most of your skills checks. You can find the familiar handbook in this blog, by using the search feature. 

Scribe Scroll ^PHB: Wizards receive this item creation feat at first level for free. It is especially useful at the start of your carreer, where you can use it to craft some cheap scrolls to use on your daily encounters (a great spell for this is Symbol of Pain, from Races of the Dragon). Later, you can use it to create some utility scrolls, that are situationally useful and good to carry around, but not good enough to memorize them daily. 

Bonus Feats: Wizards get some bonus feats at 5th and every five levels thereafter. The feat must be a metamagic, item creation feat or spell mastery.
Spells: Wizard's greatest asset is their spells. They will be discussed extensively in a later section.

Schools of Magic:

An interesting wizard feature is the ability to specialize in a certain school of magic by giving up access to others. By doing so you gain a mild bonus to spellcraft checks to learn a spell from his speciality and an extra spell per spell level, but they can only be used to store spells of your chosen school. In addition, you must spent one of your two free spells known per level on a spell from your speciality school. So, is this worth it or no? Consider that by specializing you gain an extra 45 spell levels, which is a significant amount. The main problem to this however, is which schools to give up.
The best choice if your spell selection isn't limited (as in, you have access to spells outside the SRD, like spell compendium) is to be a diviner. What is great about diviners, is that they only give up one school to specialize, while all other specialties require to give up two. The other specialities that are worth it are conjurers and transmuters, with a slight personal preference towards conjurers. The other schools are usually not worth it as specializations, because they either lack utility and answers to different threats, or because they are very good candidates for banning. In certain cases specialization in another school might work (for example getting illusion as a Shadowcraft Mage), however in general they won't work as conjuration, transmutation and divination will.

Abjuration: This school is all about protect, block and banish. Some of the most useful spells are contained in this school, especially defensive ones. It is considered a poor choice to give it up, because you lose the extremely useful Dispel Magic spell. Another good line of spells is the Protection from X and Magic Circle versus X, which protect you from mind control and summoned monsters.
Conjuration: Another useful school that contains spells you cannot give up. Dimension Door, Teleport, Summon Monster and Gate spells are considered top quality.
Divination: This is the only school you are not allowed to give up.
Enchantment: This is the first option of your potential banned schools. It has a series of spells that are useful and probably irreplaceable, like Dominate and Charm spells. However, other spells in this school, which includes mainly buffs and disabling spells, are easily replaced by other schools.
Evocation: This school includes mainly direct damage spells. Although it isn't worth it, it is generally popular to new players. Even if you need evocation spells, Shadow Evocation/Greater can help emulating them. The most useful spell of this school is probably Contingency and while it has other good spells, this is the best choice of a prohibited school probably.
Illusion: This is usually suggested as a prohibited school, but you lose great spells like Invisibility/Greater, Shadow Conjuration and Shadow Evocation. I think it's a poor choice to give that up.
Necromancy: This is a school, that although it has spells that are useful, providing you with a variety of tactics (Fear, Enervation, Ray of Exhaustion), buffing you (False Life), outright killing people (Finger of Death, Wail of the Banshee) or being the base of some potentially broken stuff (Clone, Magic Jar), you can actually drop. 

Transmutation: There is absolute no way to substitute this school's spells. It contains a wide selection of utility, combat and social spells you just can't pass: Enlarge Person, Alter Self, Spider Climb, Blink/Greater, Fly, Haste, Polymorph, Polymorph any Object and Shapechange.

Thus your best choices to dump, in order of easier-to-drop to harder-to-drop: 

Evocation

Enchantment

Necromancy

Illusion = Abjuration 

Alternative Class Features:

Immediate Magic ^{PHB II}: This ability is ranked as a very good trade, but that is true under a certain condition: you being a conjurer. The conjuration ability is immediate action teleport, which is nearly broken; you can evade attacks, get out of the range of sneak attackers or area-of-effect spells, get into position and that's only a few of the possibilities this ability can be used for. You can easily regain your familiar by spending a feat on Obtain Familiar. The other abilities gained by this alternative class feature are either lacking in power or their assosiated speciality is too weak to justify the trade of your familiar. 

Focused Specialist ^CM: This has its applications, but isn't generally worth it. Having three schools banned and three of your specialist school per day, may be handy. Although I haven't changed the color rank on this alternative feature, I've learned from experience that it's a lot better than it seems to be. First of all half of your spells known (from your wizard levels) are going to be spells of your speciality (check above, in the schools and specialization entry), which means that the loss of the generalist slots is not going to hurt that much, assuming you're specializing in a school that's worth it (conjuration, transmutation, divination). For example, a focused conjurer will have a lot more slots per day to spend on summon spells, making it easier for you to go through the daily encounters. Still, I think that the trade is pretty much equal and that you should first check if you can use the Domain Wizard alternative class feature from Unearthed Arcana, which is hands down the best.
Drakken Familiar ^DM: Your familiar gains the dragonblood subtype and gains a breath weapon instead of the ability to deliver touch spells. Pretty much equal, depending on your ability scores. Since your familiar is now dragonblood, you can use psychic reformation to give it Dragonic Aura from Dragon Magic, to benefit your party (or even you, if for example you choose the Power or Energy auras from the same book). Since your familiar is dragonblood, it can also benefit from certain spells or effects, most of them can be found in Races of the Dragon and Dragon Magic.
Wizard of Sun and Moon ^Dungeonscape: This is a bad feature. You trade your familiar for the ability to cast different spells per day depending on your surroundings. Not the best alternative feature, but it's not worthless, either. It's a good thing to be able to split the spells you can cast (although only one spell per level can be selected to be the union of sun and moon), but you've got to split them based on a night/day or indoors/outdoors theme, which is not that easy. This feature increases your usefulness, as you will find that you've got more spells that are applicable to the situation you're currently in, for example, a Daylight spell might not be that good during the daytime, but at night it's a lot better; or a huge area of effect blast might be better as an outdoors spell, because indoors it can potentially harm your teammates. Still, I prefer the benefits of a familiar to this feature.
Domain Granted Power ^CC: For the price of one bonus feat gained from wizard levels, you gain the power of a cleric domain of your choice. It is unclear if you can choose this alternative class feature multiple times (for each time you get a bonus wizard feat - it does say level 5, 10, 15 or 20) or just once; either way it's a powerful feature. Note that due to the wording that some domain powers have (they mention the word Cleric or the ability is linked to Cleric Levels) they might be worthless for you to pick, even though they might actually be incredible to a normal cleric (for example Magic domain or any domain that gives you skills). Good choices are the Luck domain (rerolls are always awesome); the Deathbound domain for necromancers (note: I'm not suggesting you should be a specialist necromancer, any wizard can create undead assuming he hasn't banned the necromancy school); the Dream domain for getting immunity to fear effects (although you can get this by carefully selecting your race - for instance undead creatures are immune to fear effects); the Inquisition domain grants you a flat unammed +4 bonus on dispel checks; the Liberation domain grants you slippery mind (and you probably have enough will save to make it useful, if you rolled badly the first time), which is a special ability for rogues (which means that they get it at levels 10+); the Oracle and Summoner domains grant a caster level bonus on divinations and conjuration(calling or summoning) respectively, at +2 instead of the usual +1 and both are worth taking if you're specializing in those areas; the Pride domain gives you the ability to reroll 1's on saves, which means that critical failure on saves is over for you; the Undeath domain gives you extra turning, which might give you turn undead, as you normally cannot turn undead, but you do get four extra attempts (consult your DM); the Dragon Below domain from Eberron Campaign Setting grants you augment summoning as a bonus feat, so you don't have to spend one feat slot on a worthless spell focus(conjuration); the Warforged domain from Faiths of Eberron grants you the ability to rebuke constructs, which is a quite broad category and full of potentially useful creatures (since you've got access to conjuration(calling) effects, you don't even have to encounter them - just call them - for instance, with planar binding); the Transformation domain is awesome for any wizard and mind blowing if you're a transmuter. A bonus hidden under the special entry of this alternative feature is that if you gain levels in a class that grants you a domain choice you gain the full benefits of this domain in addition to the other domains available to you from that class, so you can dip in a prestige that offers a domain choice (unfortunately - i'm guessing that classes that grant a single domain won't do - consult your DM) and get the spells that are granted by the domain, too.
Spontaneous Divination ^CC: So, for the price of just one feat you get to spontaneously cast a whole school of magic, which is not only useful and powerful, but also the one you're not permitted to ban (so this alternative class feature can be used by all wizards). This ability is so good that if I had used my 5th level wizard feat on another feat or alternate feature, I'd spent an extra 5 levels in the wizard class just to get it. It has been a debate whether you can cast any wizard spell you know, on your spell list or any divination generally. My interpretation is that you can cast any divination spell spontaneously, only if it appears on your spell list or you have it as a spell known (so that you can benefit from feats or features like Arcane Disciple - which gives you some spells as spell known, but doesn't actually modifies the wizard spell list). This feature will remove the need of buying and learning spells (or spending your level-up additional spells known) of the divination school completely, which will in turn give you a greater selection of spells known from the other schools of magic. To sum it up, this feature saves you gold and grants you great power by making your spell choices more versatile both passively (spell selection on level ups and from scrolls) and actively (casting a divination spell that you need spontaneously, without delay).
Abyssal Specialist ^DotU: This ability enables you to specialize not in a particular school of magic, but on spells that have the chaotic, compulsion, darkness, evil or fear; since this group of spells is now considered a school of spells for you, you can also gain Focused Specialist with Abyssal Specialist, since the latter only requires you to drop just one school of magic (like a specialist diviner). Abyssal Specialist has great synergy with the 10^th Planar Wizard substitution level, which gives an additional alignment descriptor (good, evil, chaotic, lawful) to your spells; you can choose [chaotic] or [evil] and essentially transform your specialist spell slots to generalist spell slots (since the descriptor is applied to all your spells). In addition you can use mechanics like Spell Focus[Evil] and Chaotic Spell Recall to great effect.

Substitution Levels:

Gnome Illusionist ^RoS: While nothing important changes from class skills, bonus skill points or hit die point of view, these levels really provide nice abilities and it's a great base for shadowcraft illusionists ^RoS. Remember that you must be a specialist wizard in order to pick these substitution levels.

1st level: You get silent image as a 0-level spell, which is great for shadowcraft illusionists ^RoS (actually silent image is a great spell and any caster would benefit from this ability, but shadowcraft illusionists are making it really shine). Combined with Earth Spell ^RoS and Heighten Spell ^PHB you get a further level boost when you're using your Shadow Illusion ability and thus you're able to mimic even more powerful effects. On top of that you also get other illusion spells at a lower than normal level. All these cost one caster level less in a school of your choice (it can't be banned and you have to select from evocation, transmutation or conjuration - you will probably end up with conjuration as you won't cast a lot of spells - you're better off using Shadow Illusion), so you will be able to make use of other alternative features, too.
5th level: The ability to double the duration of illusions. As an added bonus, if the spell has duration concentration, you get a 1d4 bonus to its duration after you stop concentrating on it. The tradeoff is the 5th level wizard feat and the two free spells known at that level. It is good, but unfortunately there are far more better substitutions for this level that free extend on your illusion spells.
10th level: Nice ability, but not anything to die for. Also this halts you from acquiring prestige classes.

Elven Wizard ^RotW: There are two points to this. First you cannot specialize, which is not automatically a problem, but it does limit you. Second you need to be an elf. These substitution levels are probably the best out there for non-specialist wizards, especially the first one, to which you lose virtually nothing. The elven wizard levels are very good with Domain Wizards from Unearthed Arcana, as you're technically not a specialist. As an added bonus you get search as a bonus class skill.

1st level: You get a bonus spell known at each level and a spell slot at the highest you can cast, making you unable to specialize.
3rd level: Double your familiar's granted bonus, but your familiar loses the ability to deliver touch spells and the ability to speak with animals of its type. Generally this significantly reduces your familiar to a more passive role, but the bonuses are great and variable. The familiars that grant a bonus on your saving throws (fortitude for instance) are especially good targets if you plan on getting this substitution level. Note that this feature is not good if you plan on acquiring an improved familiar, because they don't grant any bonus to their master.
5th level: What makes this level great is that even if you don't pick it, it gives you extra versatility. It may come handy to choose a different feat than your wizard ones, to fulfill requirements or get in a prestige class earlier.

Planar Wizard ^PlH: These substitution levels have two main problems. One, you need to travel regularly through the planes for them to be effective. Two, most of the levels come in mid and late levels, forcing you to take many levels in the class.

6th level: Your spells are unaffected by the impediment that a plane's magic traits apply to your spellcasting. You can actually cast impeded spells by succeeding on a spellcraft check of 20+the spell's level, which won't be difficult for a plane hopping wizard (assuming he's level appropriate to cast plane shift) and you can also spend that slot you were about to trade for an Avoid Planar Effects spell (from Spell Compendium) if need be, so that to actually avoid harmful planar effects of other planes.
10th level: This is a pretty strange ability, as ways to apply a descriptor to your spells is not easy to come by. The bonuses versus opponents of a different alignment are mild to make a big difference at these levels, but you can use this this ability effectively with stuff like the feat Spell Focus(Good or Evil) and the Chaotic Spell Recall feat from Fiendish Codex I. However you have to invest a whole lot of wizard levels to get this (not to mention the feat and the two spells known you're losing), so unless you've got a really neat trick up your robes, don't try this.
14th level: This has potential for really broken effects, but you really have to take fourteen whole levels as a wizard. Another point is that you lose a 7th level spell slot to this, which is not that hot. Lastly, it takes a standard action to channel the planar essence, making it not very helpful in combat (unless you are using quickened spells or swift/immediate/free action spells). Actually this level is a lot worse than I thought it would be after play-testing it. First of all it screams 'enhance my buff routine' and that's only true about specific spells, since you're limited to selecting a single plane at the time you acquire this ability. You can actually use this with the astral plane and use it before an encounter to launch two spells (spells cast in astral plane are enhanced to be quickened), but this tactic is really weak for the trade (your seventh level spell slot received at 14th level). If you want to receive the enhanced magic traits of a plane, consider casting Plane Shift. 

Changeling Wizard ^RoE: Changeling wizard substitution levels give extra skill points, extra class skills (bluff, disguise and sleight of hand) and interesting abilities.

1st level: The important ability in this level is dual specialization. If this means that you must absolutely specialize, then it isn't that hot. However if you can choose if you want to specialize or no, like normal wizards, this level is of top quality. Actually since it states that: This substitution feature replaces the standard wizard's specialization option. you can discard it if it doesn't suit you. As a note, dual specialization may be interesting in conjunction with focused specialist ^CM, according to how your DM interprets it. Bottom line, if you are a changeling, this is of top quality.
5th level: Limited Spell Knowledge does limit your selection, but it nets you a bonus spell, of schools that are important. However the important ability this substitution level provides is morphic familiar with which you literally acquire every familiar in the book. The selection can be really huge if you count in the improved familiar feat, too. The main problem to this though, is that it doesn't mention which abilities are acquired by your familiar's new form. Still, you do gain the granted benefit, which can prove great based on the situation you face, as your familiar can alter its form as a full-round action.
10th level: A slippery mind-like ability for transmutation spells. If you are going for this, you are going to be taking quite a few levels in the wizard class. It's nothing to die for (it doesn't protect you from spells of instantaneous duration, too, which rules out effects like Disintegrate) and it's not that good to warrant the loss of your feat.

Dukar ^CoV: Dukars are a nice idea, but in fact they suck. They give you a bonus class skill, swim, and various abilities that are either useless or require to many levels in the wizard class to be effective.

5th level: Lose your standard spells known gained. You get two bonus spells but only from two selected schools, chosen when your first dukar level is gained. Also gain a claw that can be extended and retracted as a swift action by giving up your bonus feat.
10th level: Again gain the special bonus spells the dukar get and a coral power. All the powers from the list seem useless, none are worth the exchange of a feat.
15th level: Ditto.

High-One Warrior Wizard ^CoV: These substitution levels are from the Champions of Valor Web Enhancement. These are actually multiclass substitution levels, since you need at least two paladin levels to acquire them. They offer diplomacy, handle animal, heal and ride as bonus class skills. With the cityscape web enhancement, you can trade ride and handle animal for gather information and tumble. These levels are too build specific to be any good.

2nd level: You get to stack your wizard and paladin levels to determine only how many times per day you can use your smite evil ability. Even though this only costs a 1st level spell, remember that you don't get your wizard level as a bonus to damage and your charisma bonus isn't going to be high enough to help your attack roll. Also note that smite evil requires a melee attack.
4th level: Give a second level spell to reduce arcane spell failure by 20%. This combined with other arcane spell failure reducers, can even make you able to wear heavy armor.
5th level: Interesting for alternative supermount builds, however it is bad for two reasons: Your wizard and paladin levels don't stack for the abilities of your pets and you need to progress your paladin levels to five to get a special mount.

Wizard Variants:

Combat Wizard ^UA: Lose your Scribe Scroll ^PHB and bonus wizard feats, and gain fighter bonus feats at 1st and every five levels as wizards do. Great for fulfilling requirements and to the gish types. Moreover you can choose it to get rid of Scribe Scroll for a combat feat like Improved Initiative that is a lot more straightforward and useful at later levels. Other feats that can be acquired to fulfill requirements are Point Blank Shot or Weapon Focus. Note that you can probably use this variant in addition to the alternative class features that trade your 5th level feat, so you won't be stuck up with a fighter feat at 5th level. In addition, if you're able to use Tome of Battle, you can pick the feat Martial Study (or Martial Stance at later levels), which will provide you with one low-level maneuver and give you the assosiated skill of the discipline as a class skill for all of your classes (future classes, too). Check the feats section of the guide for a detailed look at the sublime way disciplines.
Domain Wizard ^UA: By giving away your ability to specialize, you can be a domain wizard. You gain an extra spell per level and add a domain spell to spells known when you are able to cast it. Apparently you don't give up anything and there are domains with really good spells. In addition spells casted from your domain slots get a +1 bonus to their caster level. The most powerful domains are Conjuration, Necromancy, Storm (just for stealing the destructive power of Control Winds from Druids is enough to make this worth it) and Transmutation.

Specialist Wizard Variants ^UA

These variants trade the bonus wizards feats, your familiar or your specialist wizard slots for various effects that are thematically linked to a school of magic. Note that if you do give up your familiar, you won't be able to get it back by taking the Obtain Familiar feat, because it mentions that you permanently give up the ability to obtain a familiar, even from other sources. Giving up your bonus specialist spell slots is one of the worst trades you could do (you are a specialist wizard for the bonus slots - right?).

Abjurer Variants:

Resistance to Energy ^(Su): Once per day, by giving up your familiar, you gain resistance to a selected energy type equal to 5 plus 1/2 of your abjurer class level. It lasts for one hour. That's a very bad trade for a great feature, such as a familiar, which is also very easily emulated by just casting a spell.
Aura of Protection ^(Ex): Raise a protective barrier against the first attack or spell that will target you. You gain a deflection bonus to your armor class and a resistance bonus to all saving throws equal to your intelligence modifier. To gain this ability you give away your bonus feats. Whenever you gain a bonus feat, you get an additional use of this ability. This is not even close to the alternative class feature you can get instead of this; it's also very easily emulated by casting a spell.
Spontaneous Dispelling ^(Ex): By giving away your bonus spells normally gained by being a specialist, you gain the ability to lose prepared spell energy to cast dispel magic or its greater counterpart. The downside to this is that you spend one more spell level to cast it spontaneously, but you can use a readied action to counterspell.

Conjurer Variants:

Rapid Summoning ^(Ex): Trade your familiar to reduce the casting time of summon monster spells to just a standard action. This is actually a very nice ability, despite the fact that you are losing your familiar. Remember that since Summon Monster X requires a full-round action to cast, your summons will be available at the beginning of your next turn while using this ability your spell will take effect immediately.
Enhanced Summoning ^(Ex): This is a good trade. You give your bonus feats away, but you get augment summoning ^PHB as a bonus feat at first level. At later levels your summons get harder at being dispelled and additional bonuses to their strength and constitution. Especially if you plan dipping wizard, augment summoning seems a lot better than scribe scroll.
Spontaneous Summoning ^(Ex): Lose a spell to cast any summon monster spell of lower level. You trade this for the extra spells normally gained for being a specialist wizard. Unless you want to fulfill a requirement for a certain feat or prestige class, you can't normally access due to lack of summoning spontaneously, this is ok but otherwise below average.

Diviner Variants:

Enhanced Awareness ^(Ex): By giving up your familiar you gain a number of small bonuses, none of which are important.
Bonus Feat List: This does give you additional options, but i can't see how you could use it if you don't want to fulfill requirements. The best feat provided is probably improved initiative and blind fight, which is listed as a requirement usually.
Prescience ^(Ex): Add an insight bonus to any attack roll, saving throw, skill check or level check you make once per day plus one for each five class levels. This is a special immediate action, a free action that can be taken out of turn effectively. As a trade, you lose your additional spells for being a specialist wizard. While this is a nice ability, the trade off is questionable.

Enchanter Variants:

Cohort: Give up your familiar and gain a cohort plus additional bonuses if you select the Leadership ^DMG feat. Nice alternative to your familiar, but note that you will gain the cohort at 6th level.
Social Proficiency ^(Ex): By giving up your bonus feats you add many skills to your class skill list and a +2 competence bonus on checks involving one of these skills (bluff, diplomacy, gather information, intimidate and sense motive). Every five levels thereafter you gain an additional bonus to a different skill. Great if you plan to have less than five levels as wizard and want to get an expanded skill list.
Extended Enchantment ^(Su): Usually enchantment spells have nice durations and losing your additional specialist spells is a bad trade to just extend enchantment spells.

Evoker Variants:

Energy Affinity ^(Ex): +1 caster level with a chosen energy type for the price of your familiar. Not worth it at all, since there are even feats that do the same job a lot cheaper.
Energy Substitution ^(Ex): A free action that can be used once per day for each five levels attained, lets you change the energy descriptor and the effects of a spell to that of a different type.
Overcome Resistance ^(Ex): Lose your extra spells as a specialist wizard for the ability to lower a target's resistance to energy as a free action. The times per day that this can be used are enough, but the downside is that it only applies to a single target. In any way i don't think that it's worthy of the trade.

Illusionist Variants:

Chains of Disbelief ^(Ex): Opponents can't help other creatures disbelief your illusions. You have to give up your familiar to this, and while it is a nice ability i doubt that it is competent. It might be worthwhile for characters like Shadowcraft Illusionists.
Shadow Shaper: This feature offers some interesting abilities at later levels, but only a few bonuses in the start. The hide class skill can help fulfilling requirements. The 5th level ability isn't worth the trade of a wizard feat however, and the rest abilities are a pretty much equal trade. This ability is worthless, as it just gets you hide as a class skill and your intelligence bonus on your hide checks, which is very bad. Sure, the 20th level ability is awesome, but to get it you have to be a straight wizard without prestige classes, so you're actually losing the class features they would provide.
Illusion Mastery ^(Ex): This is actually one of the few alternatives to your bonus specialist spells that is an even trade. Not only you gain two bonus spells known when you unlock a new spell level, but you also master them as if having Spell Mastery ^PHB with them. That nets you 18 spells known and mastered for your 45 total spell levels (your bonus spell slots for being a specialist). Some builds may even benefit more from the mastered spells (such as Magelord ^LEoF builds).

Necromancer Variants:

Skeletal Minion: This is worth the trade. The skeleton can use weapons since it was a warrior in its previous life and has the normal undead qualities. The important part is that "The skeleton has a number of Hit Dice equal to the necromancer's class level", which is perfect, since it will gain actual hit dice and advance its saves (but not skills or feats). The minion also gains some extra bonuses based on your level. The two abilities are pretty much equal, but note that you don't lose anything for losing your minion (like experience points). Also note that it can probably be awakened, but that's a DM's call. If you can awaken it, by all means do it, because it will then be able to take feats and skills, for example Lifesense ^LM.
Undead Apotheosis ^(Ex): This is a bad trade. Sure in the end you wind up with light fortification ^DMG, but you do have to take twenty levels of wizard and lose all your feats to abilities that only add bonuses to saving throws. The 10th level ability is nice in some situations though.
Enhanced Undead ^(Ex): Nice ability which buffs up your undead even more; especially those two bonus hit dies they receive that don't count against your undead hit die limit, are a very good bonus. Keep in mind that the bonuses to attributes are enhancement, which don't stack with other enhancement bonuses. As a trade you give up your specialist bonus spell slots.

Transmuter Variants:

Enhance Attribute ^(Ex): Give up your familiar for an ability that can give a +2 enhancement bonus to one of your attributes "on-the-fly". You gain additional uses of this ability, but unfortunately the bonus doesn't scale. It would be considerably stronger if the type of the bonus was unnamed. Definitely not worth the familiar trade.
Spell Versatility ^(Ex): Not only you can make a certain spell available to you by choosing a spell from a prohibited school, you also make it transmutation, probably gaining additional bonuses (such as caster level). Worth the trade and makes specialization easier. Actually, if you have access to sourcebooks from the Faerun campaign setting and especially the Lost Empires of Faerun book, you can pick the Spell Reprieve, Item Reprieve and Arcane Transfiguration line of feats to essentially gain a whole school of magic back at a much earlier level (as early as specialist wizard level 10).
Transmutable Memory ^(Ex): So you can load up rings of wizardry ^DMG and pearls of power ^DMG of low spell levels (which are definitely cheaper) and prepare higher level spells? I would definitely trade nine 1st level spells for a 9th level one. The loss of additional spells isn't worth it though, although you do get to memorize spells from other schools. Unfortunately I missed the 'up to a maximum total equal to half his class level', which makes this ability worthless (assuming you don't want to stay more than five levels in the wizard base class, this ability lets you prepare an additional second level spell). In addition, you're giving up your bonus wizard slots, which is a lot more than what you would get by this (a normal specialist wizard will have a bonus 9th level spell at level 17, but one using this would have to wait until level 18 and he will have to sacrifice lower spell slots).