Some of my favorites:
Spartucas: The best old epic I've ever seen, and a great, yet sad, ending. Too bad Kubrick hated it. Love the music score.
2001: A Space Odysee: This sparked my interest in Kubrick's movies, and made me long for sci-fi that makes you think.
Enemy Mine: One of the most under-rated sci-fi movies of all time. Dennis Quad is one of my favorite actors, the make-up is amazing, and the plot is great too.
Watership Down: When I first saw it, I was somewhat disturbed. But this movie, I think , sparked my interest in 'serious' animation.
Steamboy: This movie is probably my favorite anime movie.