Familiars have an empathic link to their wizards. That makes them one of the best "guard dogs" around, especially if you want to keep things quiet until you get your bat guano ready. Imagine a traveling wizard with a dog that never barks, but they always seem to be aware of trouble before it strikes.
Allow the familiar to grant certain powers to their master that is appropriate to a magically gifted creature of its type. I had a goblin sorcerer with a chameleon familiar once--I granted +10 to hiding when the goblin is within 10' of the chameleon, and not moving.
Allow familiars to act like magical vessels which can store an additional spell of the caster's (or familiar's) choice. Personally, I like the idea of the familiar being free enough to choose something it would find useful for itself--it shouldn't feel completely enslaved by the wizard IMO. Additionally, you might allow the familiar to spontaneously cast any one spell (i.e., any spell from the spellbook, no memorizing)--a big difference, but one that makes it incredibly valuable to a wizard.
Allow familiars to grant a free spell penetration feat to the caster. Or, allow familiars to grant a metamagic feat X times per day like a metamagic rod.
Grant familiars the ability to have a "fighting form." This is kinda corny, but it is not unlike Battlecat from the old He-Man cartoons. This can be anything from a simple enlarge spell-like effect along with a combat oriented feat/ability [sneak attack, fly-by attack, or stunning fist-like attack are good], to adding a special ability, like a bat that can deliver a minor sonic attack. Try not to overshadow Druid animal companions if you go with this idea. Special attacks that don't require melee, and that are minor in effect are best. I always liked the idea of a Blink Dog as a familiar.
I always liked the idea of a wizard learning his spells from his familiar. What? You think only humans know magic? Granted, they no longer have the kinds of voices, and hands needed to cast their magic, so they are left with teaching a "student" wizard to show their true abilities. If you go with this, then ALL wizards would have a familiar (at least if they want to improve in level), and familiars might have other familiars as rivals or even friends...which means the wizards will quickly have rivals or friends. I would treat familiars as outsiders in this instance, and have them in their predicament because they are serving out a punishment granted by a higher power.
Allow familiars to come from forms besides an animal type. If you don't mind insects, then a queen bee and her native swarm could act as familiar (really just the queen)--which makes for interesting conversation to say the least.
Hope that helps.