Via The Little Professor, this is John Scalzi's list of the most influential science fiction movies ('The Canon' or in other words, 'the 50 science fiction films you have to see before you die'). I've bolded the ones I've seen.
The Adventures of Buckaroo Banzai Across the 8th Dimension!
Back to the Future
Bride of Frankenstein
Brother From Another Planet
A Clockwork Orange
Close Encounters of the Third Kind
The Day The Earth Stood Still
Escape From New York
ET: The Extraterrestrial
Flash Gordon: Space Soldiers (serial)
The Fly (1985 version) (I like the 1958 one better; but, then, I'm a fan of Vincent Price)
Ghost in the Shell
Invasion of the Body Snatchers (1956 version)
Mad Max 2/The Road Warrior
On the Beach
Planet of the Apes (1968 version)
Solaris (1972 version) (much better than the newer one; it requires immense patience to watch it, though)
Star Trek II: The Wrath of Khan
Star Wars Episode IV: A New Hope
Star Wars Episode V: The Empire Strikes Back
The Stepford Wives (I'm presuming this is the original, although I've seen the new one, too; the original is much better)
Terminator 2: Judgement Day
The Thing From Another World
Things to Come
28 Days Later
20,000 Leagues Under the Sea
2001: A Space Odyssey (The first time I watched this movie I fell asleep seven minutes into it. Much later I did manage to watch it again, though.)
La Voyage Dans la Lune
War of the Worlds (1953 version) (very awesome)
So that's it; only 26 out of 50.
There should also be a list of SF movies that almost no one ever watches but are very good anyway. It would be a very controversial list, I imagine, since so much of it would depend on individual taste. I would nominate Riddler's Moon, The Cold Equations, Colossus: The Forbin Project, and Dark City.