1.) Toy Story 1
2.) Up*
3.) WALL-E*
4.) The Incredibles
5.) A Bug's Life.
My favourite short is probably La Luna, or Geri's Game.
*) These come with footnotes, because who doesn't like footnotes? XD I consider the first ten minutes of Up to be some of the best visual storytelling Pixar has ever done; with an absolute minimum of dialogue, they tell us the story of an entire LIFE two people shared. That's amazing.
And re: WALL-E - I adore it for much the same reason as stated above, and I do feel it loses a bit of its charm once people are introduced (I'm here for the cute robots, okay?), but it's still a very good movie.