This is in chronological order. Also I know that there are films that deserve to be on this list that aren't. In some ways this is more of a "favorite" list than a "best movie" list.

The Day the Earth Stood Still (1951) - The first sci-fi movie I remember watching. While I haven't watched it in years I would have been remiss not to include it.
Them (1954) - This is my all time favorite giant irradiated monster movie. I rank it higher than Godzilla mainly because this was actually scary to me and that ant noise still creeps me out.
Planet of the Apes (1968) - I love this movie (the whole series really) in an unholy way. I got the boxed set which included a behind the scenes doc on making all of the monkey movies and that just deepened my respect.
Alien (1979) - Sci-fi and scary just go together so well, don't they? I remember seeing this as a kid and still have the emotional scars to prove it. I couldn't really make a successful argument as to which is better, this or its sequel, but I really wanted another 70's movie so this won.
Mad Max 2: The Road Warrior (1981) - I think this is the best of the Max movies to paint the picture of just how far the world has moved on. That plus the boomerang kid sold this completely as being numero uno.
Blade Runner (1982) - Several movies have tried to capture the truly odd worlds of Phillip K. Dick and I think that this is the only one that has really succeeded so far. That plus the really noir feel that it has and the fact that it starred Harrison when he still had something going on made this an obvious choice for me.
Ghostbusters (1984) - Okay so I had to include one movie that was intentionally funny. I love Bill Murray and all the gang and I think this is a strong choice.
Brazil (1985) - I saw this thing on video store shelves for years and always said no. Then a good friend gave me a copy and I watched it and... well I'm glad I did. Gilliam likes to do things that not only push the boundaries but kick them in their teeth (do boundaries have teeth?). If you haven't seen this, then you must rectify that immediately.
The Fly (1986) - I almost gave this slot to the original. I was like this close. You can't see how far apart I'm holding my fingers but it's really close. Making it hard to type really. Anyway, then I remembered that this movie is just better. Sometimes a remake is not a bad thing.
The Iron Giant (1999) - I had to include an animated flick and this one always brings me closest to tears of any other movie. It captures the essence of fifties sci-fi and distills it into something pure and magical. And Vin rawks.

Probably should be on here:
John Carpenter's The Thing - I have just never been able to get into this and I realize that that's a character flaw on my part.
2001: A Space Odyssey - Long. Boring. Pretentious. Or I'm an idiot.
The Incredible Shrinking Man - I know that this is a good movie, but couldn't justify including it on rep alone and it had been too, too long since I've seen it uninterrupted. If I even have.
Metropolis - Silent movie. Never seen it.
Forbidden Planet - This was another one that fought for a spot. It was tussling with The Day. I think I made the right choice.
Dr. Strangelove - I don't really see this as sci-fi per se, but I love it and it was on a lot of other lists. So I stuck it here.
Gattaca - I actually really quite like this and I think that it has potential to be a classic on day. Just not yet.