Showing my age badly here, but the best Pixar movie is "Luxo, Jr." which I saw twenty-something years ago...
Yes, it's only a short, but it's got almost everything that made the later films so fantastic - and basically changed cinema completely. (And I can still remember seeing some of the early test footage for Toy Story at an Animation Festival a few years later, and the silence with which the audience responded, because we simply couldn't believe it.)
In terms of their main catalogue, my top three would have to be Toy Story 2, The Incredibles and Wall-E, in no particular order.
I was disappointed with both Rataouille and Monsters Inc., which seemed to be more about the technical innovation than the joy of character that Pixar are so good at. (Having said that, of course, they are still head-and-shoulders above almost all of the competition. I'd take MI over, say, Madagascar any day.)