Man, this is a hard one.
I've never been a fan of Science Fiction. Never have, never will. However, there are two movies nominated here that I absolutely adore, and that's Terminator 2: Judgment Day, and The Matrix. If They Live were nominated like it should have been then I really wouldn't have known what to go with, lol.
Anyways, The Matrix was a movie I saw when it first came out, and I liked it. I didn't love it, but I liked it. I never did see any of the sequels. However, about a year ago I saw all the Matrix films on sale for only $5 and decided to pick it up. A few weeks later I finally sat down and watched The Matrix, and this time around I fucking LOVED it. The sequels I thought were terrible though, but that didn't take away from the first film for me.
Terminator 2: Judgment Day is a movie I've loved since I was a child. My mom raised me to love Arnold Schwarzenegger and his movies, and T2 was easily our favorite of the bunch (though we really loved Conan The Barbarian and Red Sonja as well). I've sat through this movie more times than I can count, and it has never gotten old, and I don't ever expect it to. Also, I dig the first one, and unlike most... I actually dig parts 3 and 4 as well. So the entire Terminator franchise has a special place in my heart, but T2 is by far and away my favorite.
Man, as I typed this up... it's really not a tough choice at all, T2 all the way. I loved The Matrix, but nothing beats that nostalgia feeling T2 brings to me. I'm not sure if I would say T2 is a better movie than The Matrix, but I definitely can say I love it more, which is why it gets my vote here.