Players tend to not keep very effective track of their familiars. Where can I find (or equally what can I use as) alternative Class Features for Wizards and Sorcerers to replace Familiars which will be more interesting and exciting for the players, while maintaining class balance?
The issue in 3.5 is that (Wizard and Sorcerer, and certain other) arcane characters automatically qualify for a familiar, regardless of character concept.
If they aren't interested in roleplaying out what amounts to an additional NPC (and the DM doesn't want to either), that's kind of a problem. Although players usually don't balk at the idea of the little benefits they get from the familiar when they come up.
At low levels, the 3.5 Familiar generally grants benefits equal to a feat: A skill focus feat, toughness (for the toad), etc. PLus the Alertness feat.
One idea is that you just take the equivalent bonus of the familiar and attach it to something Non-animate (thus removing the NPC qualities of it)- for example- a tattoo or a personal Hex/charm/totem.. that the wizard might have-- that grants the exact same benefits of the Familiar.
A Wizards Tome or grimoire could be the focus of such a benefit- as long as she carries the grimoire, she gains the equivalent of a Skill focus feat (chosen at the beginning of a campaign). To account for the loss of Alertness, you might say that the Skill focus feat is reconfigurable between adventures- these are magical books, after all, able to grant advice on any manner of subjects.
Whatever you choose- I recommend that you don't go far beyond the established structure of a feat (possibly with or without alertness) as the benefit.
Check out the D20 SRD.
There are some class variants that might appeal to your players. Specifically, many of the Specialist Wizard Variants involve replacing the familiar with some other bonus related to specializing in a specific school.
There's also an option to take an animal companion rather than a familiar.
I like what Pathfinder did with Familiars. Instead of being forced to either take a familiar or ignore a benefit of your class, you can instead choose to take an Arcane Bond with an item. This item gives the caster the ability to cast any spell in their spellbook or that they know once per day. It can also be made magical without having the requisite item creation feats (must still meet other prerequisites of the magical enhancement).
If for some reason the caster loses their bonded item, they have to make a concentration check to cast any of their spells until it is replaced. A character with an Arcane Bond can choose to have it with a staff, wand, ring, amulet, or weapon.
As familiar-keeping characters in D&D 3.x are generally saddled with the often problematic d4 hit die, I've always liked the solution of trading the familiar in for a d6. It's mechanically almost identical to taking the Toughness feat (the 3.5 version, anyway), and Familiars are just about worth a feat, anyway. (Arguably, they're worth more at higher levels, but a high-level D&D 3.x spellcaster does not need any further compensation.)
The later issues of the Paizo run of Dragon Magazine had some pretty good options - if you're okay with Eberron content, there's an awesome prestige class in issue #357 (Demogorgon on the cover) that lets you take a living spell as a familiar, and it always looked to me like a terribly fun class. Because really, why cast a fireball when you can summon an animate, sentient fireball instead?
There were various class replacement options including swapping out familiars in the PHB2 and Unearthed Arcana, I believe. I hate familiars, they are lame and almost always ignored even by wizards that have them IME. They go into the magical wizard familiar dimension 99% of the time till mentioned (usually for either roleplaying or "go get the key, we're locked in a cell" purposes). Last time I played a wizard, I used the Conjurer replacement @veritascitor mentions above to get Rapid Summoning rather than a familiar and that was a huge, huge improvement.
And now I play Pathfinder, which as @MikeBohlmann mentions has arcane bonds instead. Yay!