My top three are:
Grave of the Fireflies
All of them are by Studio Ghibli with the first by Miyazaki and the other two by Takahata. Each of them extends the range of animation beyond the traditonal children’s story.
The remaining seven in no particular order:
Toy Story 2
Jin-Roh: The Wolf Brigade
Snow White and the Seven Dwarves
I include Snow White mainly for its historical importance though it’s still a pretty good film.