My favorites are Chicken Run and Wallace and Gromit the Curse of the Were Rabit.  If you're also including hybrids I also love King Kong.

I liked Coraline, Corpse Bride was ok, and Chicken Run is a classic!

Hmm, can we include short films? If so, then Harvie Krumpet is my all time favorite. If not, probably Mary & Max, Coraline, Chicken Run, The Nightmare Before Christmas, and probably a few others I can't think of right now.

Wadey wrote:

james and the giant peach...i didnt really like it tho

I disliked the live action sequences, but the stop motion sequences were very entertaining and nice to look at. The story wasn't anything great though.

JesseOffy wrote:

The book is indispensable, though. Actually, I just love all Roald Dahl's books. They all so simple and fun to read, and somehow I feel like they would each fit well into a stop motion film.

I also enjoy his books, but not all of them.