Well, since the only thing I know about you is that you're on HN, and you haven't told us what you like or don't, or what you've already watched, you're going to get a load of essentially mainstream sci-fi. But that's your own fault.
Cypher - apparently unpopular with everyone except me, but I found it a very stylish, PKD-esque exploration of identity.
The Prestige - this one you'll probably hear elsewhere. It's mostly about the lengths to which someone is willing to go to be the very best at what they do - which obviously has some relevance for the HN crowd.
Watchmen - the only movie I watch again and again. It might be different for those who lived through it, but I love the way it can effortlessly evoke a very different era, cold-war paranoia, vietnam... a real sense of change.
Children of Men - arguably this shouldn't qualify as exceptional, and there's a lot less to say about it. What it is is some very good straight-up action, and then underlying that is a tale of how people respond to the inevitability of death. It's a simple film at heart, but I found it a very moving one.
Princess Mononoke - again, a real sense of the times changing, of conflicts that have to be resolved not by returning to the status quo but by moving forward somehow. Moral complexity everywhere, with no side being outright good or evil. And a beauty to it all even amidst the violence.