I have seen every Pixar movie at least three times (with the exception of Toy Story 3, but I saw that most recently).
I really can't decide on my favorite, so I'll start with my least favorite:
Cars. I think the story is rather boring. It's not horrible, but it just seems long and not enjoyable for me. Others that I didn't like that much are Finding Nemo, Ratatouille, and A Bug's Life.
The rest are all my favorite. ;-)
If I had to choose one, I'd go with Monsters, Inc. The movie is just so creative. It's also full of lots of hidden little messages (as are most Pixar movies).
Here is my complete ranking:
1. Monsters, Inc.
2. Toy Story 3
3. The Incredibles
4. WALL-E
5. Toy Story
6. Up
7. Toy Story 2
8. Finding Nemo
9. Ratatouille
10. A Bug's Life
11. Cars