I don't know if claymation counts, but Wallace & Gromit in The Wrong Trousers would be my favorite non-Disney animated film. I never warmed up to Shrek, sorta liked Shrek 2, and I seem to be in the minority for thinking How To Train Your Dragon wasn't all that. I enjoyed Kung Fu Panda more.
If I had to pick a hand-drawn animated film, I think I'd choose Akira. Not only is it an amazing film and story, but it's just so far away from something Disney would do that I'd consider that distinction greater than choosing a Bluth film that's too similar to Disney animated fare.
Yes, I love all the Wallace and Gromit shorts and the film. Is Akira Myazaki? Because the only Myazaki Film I have ever seen is Howls Moving Castle. Which was amazing.
Ooo, nice thread! My favorite non-Disney animated film is definitely The Swan Princess. LOVE that movie! Great story, great songs and great character. Honestly though, there are lots of other non-Disney animated films that are great, some I even find better than their Disney counterparts.