www.boston.com, which I think gets its content from the Boston Globe, has a list of the 50 best science fiction shows of all time. Unfortunately, it seems like you have to click through the list one entry at a time, so here's a list of them all (without boston.com's helpful comments). (Also unfortunately the list is full of filler.)
- Star Trek (original series)
- Battlestar Galactica (current series)
- Star Trek: The Next Generation
- The X-Files
- Babylon 5
- Stargate SG-1
- The Twilight Zone
- Dr. Who
- Mystery Science Theater 3000
- Sliders
- Lost
- Xena: Warrior Princess
- The Outer Limits
- Star Trek: Voyager
- Logan's Run
- Flash Gordon
- Firefly
- V
- Dark Angel
- The Hitchhiker
- Quantum Leap
- Andromeda
- Tales from the Crypt
- Wonder Woman
- The Jetsons
- Stargate Atlantis
- Buffy the Vampire Slayer
- Adventures of Superman
- The Six Million Dollar Man
- Voyage to the Bottom of the Sea
- Alien Nation
- My Favorite Martian
- Lost in Space
- The Avengers
- Battlestar Galactica (original series)
- The Bionic Woman
- Space 1999
- Batman
- The Man from U.N.C.L.E.
- The Thunderbirds
- Futurama
- Science Fiction Theatre
- Nowhere Man
- Lois & Clark: The New Adventures of Superman
- The Greatest American Hero
- That Was Then
- Buck Rogers in the 25th Century
- 3rd Rock from the Sun
- The Wild Wild West
- Earth: Final Conflict