If you saw my list of underrated science fiction movies, you'll know that I love a good ending. For me a great ending is when the movie really uses those last seconds to add something to the storyline (or even transform your perception of the whole movie), so that you sit watching the credits trying to digest what just happened. (I've nothing against epilogue-style endings--I'm looking at you, Lord of the Rings: The Return of the King--but they're not great in and of themselves.) Again, your suggestions welcome! (Also, beware spoilers!)
Invasion of the Body Snatchers (1956, original ending). This movie brings home the bacon of paranoia as the helpless protagnist screams at the movie watching audience that they're next.
Planet of the Apes (1968) Quite possibly the best ending of a movie ever, I can still remember the shattering shock of discovering the identity of the Planet of the Apes when I first saw this movie.
2001: A Space Odyssey (1968) Sure, the voyage Beyond the Infinite is confusing, but the very final shot of the Star Baby gazing upon the Earth speaks to the promise of the future that's built into the film's DNA.
Dark Star (1974) A philosophical showdown with a sentient bomb taken to its logical conclusion accompanied by brilliant dialogue.
Bladerunner(1982, original ending) A great twist at the end, but one which met significant opposition, and the meaning of which wasn't confirmed by director Ridley Scott until decades later.
The Terminator (1984) Okay, so yes, the end of this movie does herald the otherwise depressing prospect of inevitable nuclear war, but it's defiance beautifully sums up the movie.
Brazil (1985, original ending) Yes, it's depressing. But then, did you see the rest of the movie?
Back to the Future (1985) Admittedly, it's not particularly thought-provoking, but the flying-car ending of this movie deserves its place for being just an awesome kick in pants.
Twelve Monkeys (1995) The uncompromising logic of the movie gets taken to its grinding conclusion, along with a clever little twist.
Contact (1997) I liked the idea here that the super-advanced and super-manipulative aliens that screwed the protagonist over weren't all powerful.