Some great choices but you're all forgetting about the best movie in the whole wide world ever: Avatar
But seriously, my favourite film of all time is Andrei Tarkovsky's Solyaris
Based on the story by Lem Stanislaw, Solyaris portrays an unsettling, claustrophobic tale of supernatural phenomena on a space station.
The most epic sci-fi film I have ever seen, and one that I could re-watch again and again, irrespective of its length (3 hrs).
Not too conventional, and hardly a winning pick but if you're into sci-fi and you haven't seen it, I'd definitely urge you to watch it.