Space: Above and Beyond (this one will be fun to find)

Babylon 5: The most epic story arc ever. The first season is slow, but when you realize that things said in the first season are relevant to the events in the fourth, you'll be glad you watched it. The fifth season almost didn't happen and the primary events that were scheduled for it got condensed into the fourth. So S5 feels a bit like it's tacked on, but it does stay true to the original planned story arc and covers all the stuff that got cut when S4/S5 got pushed into one season.

Farscape: OP is watching this already, but I want to recommend it to everyone. It's a great piece of storytelling and has amazing characters.

Stargate (SG1, Atlantis, and Universe were all pretty good): If you haven't seen this,watch it. You'll know you're hooked when you understand what "In the middle of my backswing???" means.

Doctor Who: Old ones are kind of tedious, new ones are awesome.

DS9 and Firefly are both great.

The DS9 Episode In the Pale Moonlight is probably my favorite.

Star wars the Clone Wars was not what I expected. Murder, Torture (Once to death), Firebombing villages full of starving civilians, mass casualties, hostage taking, blowing up hospital stations, acts of genocide, slavery... the list goes on and on. They basically said screw the sensors.

It isn't bad.

They're fairly equivalent, yes. Random crap happening on a psuedo-interesting space station, with a few episodes set to lay the groundwork for the overall plots of each series. It goes rather farther than that, though - DS9's later seasons are awash in, "Last week, on Babylon 5..."

Absolutely nothing wrong with that; it's probably why DS9 was the only Trek series with a coherent, epic plot. And it's not like JMS wasn't digging around in Tolkien's pockets for B5. Good artists create; great artists steal.

Lexx was terrible. I have no other word for it. I found Andromeda to be more tolerable.

New version of "The Outer Limits" is still my personal favourite sci-fi show.

Oh right, I remember that. I watched it, was somewhat entertained. TBH I'm surprised it got renewed. I'll have to go back and watch the first season again to figure out what I missed.

Some other stuff:

Fringe! I'm surprised no one else has mentioned it until now.

Terra Nova was a decent time travel show for the one season it aired, and actually did a pretty fair job of wrapping up the major plot and not leaving a massive cliffhanger before it got cancelled.

Eureka and Warehouse 13 are two light sci fi shows set in the same universe. They're half comedy and half adventure. Don't take them seriously at all.

Alphas is a decent "secret mutant team" show where for once the mutants aren't absurdly overpowered. No flying bridges and instant tornadoes here.

Heroes is another. Save the cheerleader and all that.

The miniseries Taken was quite good.

The X-Files, of course.

Joss Whedon's Dollhouse is one of those that some love, and some hate.

Terminator: The Sarah Connor Chronicles

Another one from around the same time as Space: Above and Beyond was Earth 2.

Earth: Final Conflict is one I keep meaning to check out.

The 4400.

SeaQuest DSV, another "classic".

Seven Days for more time travel.

Sliders.

That's all I can think of for now.

Despite being animated, Ghost in the Shell: Stand Alone Complex and 2nd Gig are pretty damn good scifi series. Even if you don't like anime, give this one a try, it's very grownup and rather complex, you may need more than one watch to get all the references and nuances.

It plays in 2029, in a futuristic Japan. The series revolves around a squad of the most elite law enforcers in the country, tackling some very high profile cases. There's a main case threaded throughout both seasons which can get incredibly complex - One of the early episodes in season 1 is almost only dialogue, but it's still pretty fantastic imho.

The rest has already been mentioned i think :)

In fact I think the episode which first introduced The Weeping Angels, "Blink" is one of the best sci fi episodes of all time.