The Forlorn flaw from Dragon vol. 333 prevents you from gaining a familiar. As with all flaws, you get an extra feat for taking it. The existence of the Obtain Familiar feat (Complete Arcane) suggests that this is a fair trade and that the familiar is valued about the same as a feat.
For actual alternate options, from the best list of alternate class features that I know of
Aquatic wizards or changeling wizards get different types of familiars, as do any other wizards who select drakken familiar, frostfell familiar, wasteland familiar, or wilderness companion.
High One Warrior Wizard (Champions of Valor) lets you replace your familiar with your paladin special mount, which gains some of the benefits a familiar would have. Requires you to be a paladin and does not actually grant the special mount feature.
Immediate Magic (Player’s Handbook II) replaces your familiar with an immediate-action, single-round effect that you can use Int mod times per day. The nature of the effect depends on the school you specialize in:
- Abjuration: Urgent Shield – +2 AC
- Conjuration: Abrupt Jaunt – short range teleport
- Divination: Glimpse Peril – +2 on next saving throw
- Enchantment: Instant Daze – Daze someone who attacked you in melee
- Evocation: Counterfire – 1d6/3 levels force damage on enemy who attacked you at range
- Illusion: Brief Figment – Single mirror image of you
- Necromancy: Cursed Glance – −2 AC and saving throws on enemy who attacked you at range
- Transmutation: Sudden Shift – Gain climb, fly, or swim speed equal to land speed
Specialist Variants (Unearthed Arcana or SRD) replaces your familiar with some other effect based on specialization:
- Abjuration: Resistance to Energy – 1/day, 1 hour resistance to energy of choice equal to 5+½wizard level
- Conjuration: Rapid Summoning – summon monster spells may be cast in 1 standard action
- Divination: Enhanced Awareness – Sense Motive as a wizard class skill, identify in 10 minutes instead of an hour, arcane eye moves at 20 ft/round instead of 10, and +1 to save DC of divinations
- Enchantment: Cohort – get a cohort, à la Leadership, but no followers, at 6th.
- Evocation: Energy Affinity – +1 caster level when casting an evocation spell of the energy type chosen at 1st level.
- Illusionist: Chains of Disbelief – Someone who succeeds on a save against your illusions cannot help others to do so, and your illusions can even fool those who have proof that they are fake (but they do get a +10 bonus on the save).
- Necromancy: Skeleton Minion – a skeleton instead of a familiar.
- Transmutation: Enhance Attribute – Swift action, +2 enhancement bonus to an ability score, lasts 1 minute/wizard level, 1/day plus another use every five wizard levels
Wizard of Sun and Moon (Dungeonscape) can prepare two spells in a single slot, one of which is only available above ground during the day, and the other of which is only available underground or at night.
Abrupt Jaunt is by far the best; if allowed (and you don’t mind making your best-class-in-the-game dramatically-more-powerful), just take it unless you are a dedicated summoner (then take Rapid Summoning) or illusionist (then take Chains of Belief). The rest are... really mediocre. Some of the other immediate magic options are OK, like Cursed Glance or Sudden Shift. Instant Daze is pretty good in a campaign where Enchantment is viable, but it often isn’t.