A Bug's Life is my "favorite", however, I don't think it was the most well-written or animated. I'm just partial to it for various personal reasons.
I think Monsters, Inc was probably the coolest for storyline. Toy Story (and its excellent sequel) for characters. I love superhero/villain stories so the Incredibles gets my vote for setting/theme. Finding Nemo was pretty but I found it a little lacking. I haven't even bothered to see Cars yet a second time.
What else did they make, lol.
I went to Cal Arts with a couple of guys who went on to work for Pixar; I always enjoy looking for their names in the credits.