Ok, gonna make big list because I watch way too much TV. 
Just about to finish:
Farscape: Space adventure show with great characters, zany humor, and outstanding production design. The first season starts out a bit “meh,” but when the story arcs begin in earnest, it starts getting really awesome. On that note, Farscape is often considered to be a successor to Babylon 5 in that it’s a space-based show with strong continuity and not many standalone episodes.
In the midst of watching:
Stargate SG-1: I think everyone and his dog knows about this show. It has a great premise (pagan gods were actually aliens who control much of the galaxy via the Stargate network), lots of intriguing episodes, and a great sense of humor. I also think it has one of the best overall groups of main characters in any show I’ve seen–there are five primary protagonists, and I think they’re all awesome.
The X-Files: another show everyone knows about. It almost seems to be two shows in one: a procedural (every episode stands on its own) show about paranormal investigators who examine all kinds of inexplicable activity, and an arc-based show about getting to the bottom of a government conspiracy revolving around aliens. Depending on your preferences, you might like both aspects, or find one or the other irritating. So far, I’ve liked both, though I hear the alien conspiracy arc wasn’t planned out and got ridiculous as time went on.
Star Trek TNG: I don’t think this show is quite as good as TOS and DS9 (it tends to be too saccharine), but it’s still awesome. Skip most of the first two seasons, though; they have a lot of really awful episodes.
White Collar: I marathoned the first three season a while back, but for some reason haven’t gotten around to the rest of it. It’s kind of a cliché “reforming con-man” show on the surface, but the character development and acting are very good. It also has some really good plots twists and gags.
Shows I’ve finished:
Babylon 5: Best story arc ever. No other show combines politics, philosophy, war, religion, and character development so well.
Star Trek TOS: Tied with B5 as my favorite show. Though it doesn’t really have much in the way of story arcs, it has outstanding character development and explores philosophy and morality better than any other show IMO.
Star Trek: Deep Space Nine: Often compared to Babylon 5, they really don’t have much in common. DS9 is a pretty straightforward war drama. I think the overall cast of characters is a bit better than B5, but the main story arc isn’t as profound. This show also does a lot of great worldbuilding, and is by far the most serialized Star Trek show.
Star Wars: The Clone Wars: it starts out a bit too childish, but it starts getting much better in the last few episodes of season 1. This show is so good, it actually makes the prequels seem like ok movies. The portrayal of Anakin is much more in line with what you would have expected him to be like if you just watched the original movies.
Doctor Who: It’s cool, I guess. Nah, IMO, this show has the best premise ever, because it allows it to tell any type of story it wants to, be it an epic space adventure, hard sci-fi, soft sci-fi, a murder mystery, a horror story, a character study, historical fiction, or all of those at once.
Sherlock: Possibly the best show currently in production. The acting is perfect and the writing is amazingly clever at updating Arthur Conan Doyle’s characters and ideas for the modern world.
Psych: Hilarious show. Sort of a parody of the standard Sherlock Homes formula.
Avatar: The Last Airbender: For a show about kids going on a quest in a fantasy world, it’s pretty good.
Chuck: This is a really fun show if you: like spy fiction, pop culture, and/or are a nerd.
