One thing you can definitely say about 2009 is that it was a crackerjack year for science fiction on the small screen!
Torchwood: Children of Earth
This was the third season (or "series three" in BBC parlance) of one of my personal favorite science fiction shows, and it did not disappoint. It horrified, disturbed, and violated everything we had learned to feel for the show's various characters, but it did not disappoint. I think I'm still a little wobbly from the finale.
Children of Earth was a super-short season of only five episodes due to the show's move to the higher profile channel BBC One. This matters little to us here in the States, but the up shot is that future seasons will presumably be of normal length.
The End of Battlestar Galactica
I'll be honest with you, I had real trouble sticking with Battlestar Galactica this season. By the time we were at the halfway mark, I was more than ready to just let it go. It had been too grim for too long, and somehow the tone just didn't seem right anymore. I only stuck with it because I knew it was a choice between watching the finale with everyone else, or having it immediately spoiled and being left out of every internet conversation for the next two months.
The finale was grueling at the time, because I was convinced that at any minute the entire fleet was going to jump into a black hole and everyone would die. (Maybe I was just scarred from having finished the final season of Angel only a few months earlier.)
Doctor Who, Series 4
I felt this was one of the strongest of the new Doctor Who seasons. I put off watching it for several months, because I was convinced that nothing could top Martha Jones' exit from the show. After watching the entire season through, I realized that I was very wrong. Although occasionally goofy (stealing the entire planet? Really?) this season had an emotional truth that was rock solid.
Stargate Universe
I have become increasingly disenchanted with SGU, but I still hold out hope for it. Many shows have a weak first season, but rally once they find their footing. (When was the last time you saw the X-Files pilot? Pee yew!) I find the plots to be leaden, and the female characters to be marginalized in the extreme. But the show has some great talent, both on and off the screen, and the set-up is genius.
Honorable Mentions
Fringe: I enjoy watching this show, even though it rarely seems to get anywhere. It's like The X-Files but completely set adrift. At the same time, the arc story makes an appearance in each episode, no matter how small, which I definitely appreciate.
Flashforward: Based on the Robert Sawyer novel, this show kind of lost me about halfway through. I look forward to catching it on DVD.
Supernatural: Everyone says this show is awesome, but I have yet to get the player on the CW website to work on my computer. Some day?
The Sarah Jane Chronicles: Surprisingly good, if you take it as "Doctor Who for Kids." Which I realize is kinda funny because Doctor Who is already for kids, but hey.
Warehouse 13: Had promise, watched a few episodes, willing to give it the benefit of the doubt.
V: Terrible.