For me the list starts strong but goes off the rails:
25 V--didn't watch it, can't judge
24 Galaxy Quest--didn't watch it, can't judge...but I'm suspicious
23 Dr Who--only saw a couple episodes, can't judge (ducks hurled garbage)
22 Quantum Leap--only saw a couple episodes, can't judge (but from roughly that era, Sliders caught more of my attention)
21 Futurama--big fan, good call
20 Star Wars Clone Wars (Cartoon)--never saw it, can't judge
19 Starship Troopers--good call; liked the book, like the movie, I don't take it as a pure repudiation of the book's politics, more as a stark questioning. A very rich film, and presciently timely.
18 Heros--never saw it, can't judge.
17 Eternal Sunshine of the spotless mind--great movie, but where's 12 Monkeys?
16 Total Recall--Arnold's best
15 Firefly/Serenity--saw one episode, wasn't crazy about it, but not enough to really judge
14 Children of Men--never saw it, can't judge
13 Terminator (1 and 2)--can't argue with that
12 Back to the Future--borderline classic
11 Lost--haven't seen it, can't judge
10 The Thing--possibly the best other than the unjustly absent 12 Monkeys
9 Aliens--another fine film
8 Star Trek the next generation--the first bad call. Mediocre science fiction, bad writing & plotting, Mary Sues right & left.
7 ET--can't complain. I'm Elliot.
6 Brazil--every Gilliam is golden (well, except for Jabberwocky), and this is SF, so...yes.
5 Star Trek 2 Wrath of Khan--I'm one of the few who preferred the first movie, but it didn't make the chronological cutoff.
4 X-Files--barely watched it, had its moments.
3 Blade Runner--good call.
2 Battlestar Galactica (The new one)--saw one episode, felt kind of meh-ish, but not enough to judge.
1 Matrix--the list was flagging, here it collapses in front of the finish line. Somewhat like the movie itself, which promises far more than it ultimately delivers. (Once the big secret is revealed, it's all downhill.)
Other omissions: Mad Max Beyond Thunderdome, The Fly (yes, it's both SF & horror), Robocop, Pi, and the TV version of Aeon Flux. Outland just barely misses the chronological cutoff.
And if we go outside of American movies, especially if we include anime, well: Macross, Macross 2, Macross Zero, Ghost in the Shell, Wings of Honneamise, Akira, Delicatessen, Nausicaa of the Valley of the Wind.