It's definitely a tie between a few different animated films I saw growing up. In no particular order:

1. Land Before Time ( specifically the first and the one where they cross the ocean to an island ).
2. An American Tail ( and the sequel ).
3. Secret of NIHM. We had to read the book in 4th grade and then we got to watch the movie. It was a blast.

It's hard for me to pick which one of those are my favorite feel-good* film.

*Feel-good as in makes me feel good watching them.