The ever-popular toad is of course every munchkins dream...
In my piratecampaign, parrot was a popular choice. (Treated as if it was a raven.)
If you're going with the Improved Familiar-feat, the coolest choices IMHO must be a pseudodragon if you're a good-guy or an imp if you're playing a not-so-good-guy.
I love the Raven. I've had a Raven, Owl and Toad as familures. I took the Own once because I was playing a CN Drow Necromancer and found a picture of a Drow with an Owl on his arm, and thought it looked cool, and took the Owl as my familure. Took the Toad once for the +2 Con Raven is my favorite though, its nice to have a familure that can talk, especially if your party gets seperated in a fight (you can have the familure with the rest of the party)
In some Dragon magazine (the Sorcery issue I believe) they had squirrels and mice and all kinds of cute very small animals. I really enjoyed my weasel as well, because I was playing a ranger/wizardish character (Arcane Archer)
The improved familiar feat is well worth it IMO, by the way. Makes your familiar a lot more useful, instead of an animal in a box.
Personally, I think you can't go wrong with a Bat. It can fly, it is at home in a dungeon and the Blindsight can be a lifesaver if you run up against invisible foes.
The last wizard that I ran was Gnoblin the Gnome and his familiar was Severus the Bat. Severus was the only survivor of the campaign.