I read about this on FilmJunk, apparently Entertainment Weekly made this list of the best sci-fi movies made in the last 25 years. It has a few good ones and a few bad ones.
Frankly comparing a television show with a movie doesn’t work for me; as one develops over a longer period of time. A quick look at this list shows the variety of overriding genres that have sci-fi elements. Futurama is a comedy, Quantum Leap was a drama (very little sci-fi). Clone Wars (which is awesome!) is an action cartoon. I don’t know about The Matrix being the best sci-fi in the last 25 years (I’ve added my opinions in parentheses). I myself am partial to Bladerunner which deals with much of the same issues with AI, etc. but does so with a fantastic neo–noir complexity that trumps the freshmen level philosophy and visual effects of The Matrix. It should be noted that Edward James Olmos plays a critical role in both the number 2 and number 3 picks on the list, once again proving that EJO is freakin‘ awesome!
25. V: The Mini-series (in the 80’s there were great shows like V but then there was also crap like V, staring the Beastmaster himself Mark Singer)
24. Galaxy Quest (meh)
23. Doctor Who
22. Quantum Leap
21. Futurama
20. Star Wars: Clone Wars
19. Starship Troopers (whaaaa? the book was alright)
18. Heroes (we’ll see)
17. Eternal Sunshine of the Spotless Mind
16. Total Recall
15. Firefly/Serenity
14. Children of Men (very good)
13. The Terminator/Terminator 2 (meh)
12. Back To The Future
11. Lost 
10. The Thing
9. Aliens (game over man but I think Alien is a better movie)
8. Star Trek: TNG (Christ this show was boring DS9 had a freakin‘ war that’s drama and action, this show was all rehash of the first series and boring diplomatic intrigue)
7. E.T.
6. Brazil (gotta love the natural blending of Kafkaesque and Pythonesque)
5. Star Trek II: The Wrath of Khan (James Horner’s score rules)
4. The X-Files (it was great until it went on too long and got lame around season 7)
3. Blade Runner
2. Battlestar Galactica (this show is the only good thing Sci-fi Channel has done since they aired Akira and Robot Carnival in the early 90’s this list also lacks anime like Cowboy Bebop and Ghost in the Shell)
1. The Matrix
According to Toonzone it looks like Sci-Fi will start airing anime again on Monday nights from 11-1. This might be cool but that’s a pretty bad day, it starts June 11th with Ghost in the Shell: Stand Alone Complex Solid State Society (that’s GITS: S.A.C. SSS for those in the know – yeah right)