Cast haunt shift on an undead familiar so it inhabits a Tiny object
You want familiars that are Tiny objects. The good news is that's possible. The bad news? Doing it takes most of your feats and it's enormously suboptimal. However, fortunately, since you need to be a full caster to do this (and probably a wizard or a sorcerer), even if you took the feat Toughness every time, you'd still be a rock star.
Anyway, this process has several parts.
On your mark: Make the familiar undead
At level 1, take the feat Stitched Flesh Familiar (Libris Mortis 30). This gives a standard familiar the type undead. It also gets a few more hp and those spiffy undead traits and…, well, not much else, really. Because at least three necromancy spells are needed to meet the feat's prerequisite, spell selection is tight, but two cantrips and ray of enfeeblement are a reasonable investment for this build even for a sorcerer. However, you just go ahead and be you. Alternatively, the feat Undead Familiar (Dragon #280 62) does what Stitched Flesh Familiar does but cheaper and weirder 'cause it's older; ask the DM.
Get set: Access haunt shift and make preparations
Obviously, you'll need the 5th-level Sor/Wiz spell haunt shift [necro] (Libris Mortis 66), so adventure normally until able to cast 5th-level spells then pick as one of them the spell haunt shift. You also need an easy way to gain negative levels. I suggest possessing an alignment other than true neutral and buying some magic arrows with a magic weapon special ability inimical to one of your alignment components (e.g. +1 holy arrows if you're chaotic evil, +1 anarchic arrows if you're lawful neutral). These arrows should each cost 366 gp 1 cp, and you'll need your level minus 8 of them.
Option: Spellstitch that familiar now!
If you want to do this, you need to do it before casting the spell haunt shift. Complete Arcane describes the template spellstitched (161-2) that can be slapped on any corporeal undead creature and, unlike many options, includes mechanics for doing it! It costs 1,000 gp plus the undead creature's Wisdom score ×500 XP. In addition to some minor (but tasty!) bonuses, it grants the creature spell-like abilities, the number and level based on its Wisdom. Because they're spell-like abilities, no XP and material component costs are incurred. Its caster level equals its hit dice, so even normally suboptimal choices work. Spells need to be conjuration, evocation, or necromancy and are limited to certain levels, but animate dead, desecrate, false life, magic jar, raise dead, spiritual weapon, and unhallow are all options in core.
You also want to get whatever doodad into which you're shoving your familiar. Said doodad should be in the Tiny-to-Huge size range. (Also, keep in mind the spell may not work if the doodad's magical.)
Go!: Cast haunt shift on the undead familiar
Drop your effective level to 8 by toting the magical arrows while simultaneously keeping a 5th-level spell. Each negative level removes one spell of the highest level you can cast, so how this works will be specific to your circumstance.
See, the spell haunt shift has some rough requirements: it's a 5th-level spell (so not normally available before character level 9), but the spell doesn't affect undead creatures with more than 8 Hit Dice. As the familiar uses for its effective Hit Dice the higher of its own Hit Dice or its master's contributing levels, by the time you can cast the spell haunt shift, your familiar isn't a valid target! Grabbing arrows for some negative levels to decrease your effective character level to 8—so that the familiar's Hit Dice also decrease to 8—makes the familiar a valid target once more for the spell haunt shift, a spell with a duration of instantaneous so it doesn't, like, wear off when that target's not valid anymore. And, because of how negative levels interact with spells, you can still cast the spell haunt shift.
For example, a Wiz9 that possesses Intelligence 20 has a bonus 5th-level spell and can cast a total of two fifth level spells. He picks up a magic arrow and gains a negative level. His effective character level is 8 and he has one 5th-level spell remaining. That spell is, of course, haunt shift.
Then put the familiar in its new home by casting the spell haunt shift on your familiar. And hoping. A lot. See, the spell turns an undead critter into a haunting presence (Libris Mortis 6 and nowhere else!). The upshot to this is that haunting presences are immune to just about everything, sometimes live in items, and can sometimes animate objects they inhabit! The downside is that the spell literally only says, "Haunt shift translates corporeal and incorporeal undead into haunting presences," then describes how many and in what order undead creatures in the spell's area are affected, leaving the details to the book's earlier Haunting Presences section… which is startlingly vague on picking what a presence actually haunts. The section says that presences can occur naturally or as the result of haunt shift, the DM maybe picking what's haunted like the DM'd place any other monster, but then the section gives rules that objects currently in a character's possession cannot be haunted, and that unattended magic items receive a saving throw. This can be three ways:
- What the presence haunts is determined by the DM. And you're stuck playing Mother-May-I. To me, this is unlikely; there should be no saving throw against DM fiat.
- What the presence haunts is determined by the caster of the spell haunting presence. If you turn an undead creature into a haunting presence, you pick the details. That makes the most sense to me, but it's unsupported mechanically.
- What the presence haunts is determined by the undead creature. It picks what it'll haunt. This matches the section's language, but it's also unsupported mechanically.
So in the second and third case, your familiar goes where you want it to. In the first case, you can still make a reasonable argument that your familiar should go where you want it to. Good luck!
(I've not played in a campaign with friendly, capitalistic necromancers willing to trade coin for spells, but if you do, you may be able to just pay one to cast the spell haunt shift [necro] (Libris Mortis 66). A Wiz9 charges only 450 gp for this, and that's a bargain compared to the hoops you have to jump through to cast the spell haunt shift yourself. You'll still need to take negative levels beforehand if too high a level, though.)
After all this, you essentially have an object that's a familiar. Technically, the haunting presence is your familiar, but it travels with the object, sees from the object's perspective, interacts with the world through the object, and basically can only be affected by messing with the object. The familiar can manifest in its original stitched-flesh form a number of times per week equal to its Hit Dice each time for a number of minutes equal to its Hit Dice, so, if it's important to you, you can still choose it like a Pokémon.
Also, if the object has moving parts, your familiar can move those parts. Printed examples include a wagon rolling and a crossbow cocking and firing. If your familiar manages a non-trivial Charisma 17, it can even animate the object as per an effect like the spell animate objects.
"Okay, that's one. Now get me four more!"
The feat Extra Familiar can provide more familiars. Probably. The feat appears in Dragon #280 and is both poorly written and 3e material. It says that you can choose an extra familiar from the PH's list or from the the article. The feat Stitched-Flesh Familiar says "when choosing a familiar, you may choose a stitched-flesh familiar." So, depending how the two feats interact, and depending how your DM feels about Dragon material, and depending how he decides to tweak it for the 3.5 revision, this may let you get additional undead familiars. The feat Extra Familiar is not usually a very worthwhile feat, and, when compared to what a wizard can do with five feats, it's certainly not game-breaking, so I'd allow it, but your DM's mileage may vary.