I'm not really into science fiction as much as I am into fantasy, but I still have seen a good number sci-fi shows as well. There are tons of shows not mentioned here that sci-fi fans love (Battlestar Gallactica, Stargate: SG-1, Star Trek), but here are my personal favorites:

#10 Sliders

In Sliders, a machine was invented with the ability to move people to alternate realities, but it malfunctioned, so now the characters are stuck constantly "sliding" from world to world, hoping that one day they will make it home to the version of Earth they belong in.

#9 John Doe

This show was canceled long enough ago and short enough that I can't remember it well, except that I was devastated when it was canceled. It had to do with a man who was a supergenius suffering from amnesia, but that's all I recall at the moment.

#8 Terminator: The Sarah Connor Chronicles

The only show on my list still running, this is a TV series based on the popular Terminator trilogy. This show is a mixed bag - fantastic actresses abound and there are some really interesting philosophical themes, but sometimes the plot seems to have huge gaps in it so things don't quite make sense. Still, you should definitely be watching it.

#7 Alien Nation

This is a show where aliens are used as a metaphor for any other minority group throughout history, and it's pretty damn cool. Plus, they get drunk on spoiled milk, which is totally LOL-worthy.

#6 V

In this show, aliens land on Earth, and do a lot of stuff that is reminiscent of the Holocaust.

#5 X-Files

As the monster-of-the-week show it was in the beginning, X-Files rocked. IMO, though, it totally jumped the shark at some point - was it when Scully was declared infertile, had a baby anyway, and then gave it away? when Mulder died? when the Supersoldiers showed up (who are exactly like Superman, except evil)? Regardless, there is still some classic television here, and it is the show to beat.

#4 Firefly

A lot of people would put this show at #1, but it's so short, I just didn't quite get enough of it for it to be that high on my list. The cast is fantastic, it's created by Joss Whedon (who also created Buffy the Vampire Slayer, Dr. Horrible's Sing-Along Blog, and the upcoming Dollhouse), and there are space cowboys involved.

#3 Dark Angel

In this show, there's an alternate history which involves the United States going into economic meltdown due to an EMP wave. Jessica Alba stars as a genetically modified soldier who kicks an incredible amount of butt.

#2 The 4400

4400 people reported missing since the 1920s are returned in a white light, and slowly discover they have unique abilities, precognition or telekinesis. The plot only thickens from there.

#1 Odyssey 5

5 people on a space shuttle called the Odyssey 5 watch Earth get destroyed in some giant fiery thing, and then get sucked through a black hole, pulled into a space port, and thrust back 5 years in the past in their old bodies on a mission: to figure out why the Earth got destroyed and how to fix it. There's all these advanced AIs, cyborgs, and nanobots, and I swear, you'll be up all night all excited and nervous from the plot. I can't believe there was only one season. It's so wrong.