I'm going to have to go with dinosaurs for my favorite D&D animals. Seriously, how often do you get to smash together a fantasy game with Jurassic Park?
Whether they're a natural part of the setting or some wizard's magical creations, dinosaurs fit all sorts of different roles. Looking for a lizardfolk equivalent for cows? Triceratops or stegosaurus fits the bill. Druid's animal companion? Why not go with a deinonychus instead of a bear? Pissed off halfling doesn't want to ride a pony? Deinonychus works for that too. An underwater adventure needs something a bit more intimidating than a shark? Throw an elasmosaurus at the party. The group needs a way to fly without using a spell? Giant pterodactyls are the answer. How about a wizard's thrall, guarding his tower? Tyrannosaurus rex seems appropriate there.
This is a short entry, but there's not much to be said here. If you want to have a more prehistoric or reptilian feel, dinosaurs are the perfect replacements for regular animals.