God Told Me To (Larry Cohen)
Because when you have a premise like God is alive and living somewhere in downtown Manhattan, you have to be a great science fiction film.
Metropolis (Fritz Lang)
Because it's one of the greatest pieces of world-building ever; because of its images of oppressed men, working like the parts of a gigantic machine--images that, to Lang's horror, would later inspire fellow world-builder Adolf Hitler.
Because Tarkovsky creates out of an orbiting space station one of the most desolate haunted houses I've ever seen; because he makes compelling drama not out of outer but of inner space (set, just to confuse the issue, in outer space).
La Jetee (Chris Marker)
Because at forty minutes it's possibly the most sheerly beautiful science fiction film I've ever seen--a series of still images, cut together, telling the story of a time-travelling man's life coming to a full circle.
Nausicaa, of the Valley of the Wind (Hayao Miyazaki)
Because it's that rare creature, ecological science fiction; because its science is more solid than in most anime; because it features that most difficult of all heroines to portray (in an interesting manner)--the truly good person--and because, rarest of all but especially in science fiction, it's so moving. This would be my favorite, I think.