I really, really hate the EMH (VOY). I mean, he just grates on me no end. And Picardo's character on the Stargate shows isn't much better, so it might be just as much Picardo as it is the EMH. But I really hate the EMH and find him to be incredibly annoying. I mean, I really detest this smarmy, smug, and utterly annoying character.
Runners Up include: Byron (
Babylon 5), Teyla (
Stargate Atlantis), Neelix (VOY), Wesley Crusher (TNG), Xander (
Buffy the Vampire Slayer), Lana Lang (
Smallville), River Tam (
Firefly), and Tess (
Roswell). I also really detested Baltar and Six in season 1 of
BSG (I almost quit the show because of them), but they got better later on and I like them okay now.
Also, strain as I might, I find pretty much all the male characters on
Torchwood to be incredibly annoying. I like the girls, but the guys on that show are quite annoying.
And finally, pretty much any character played by Kevin Sorbo is a non-starter, in my book. The worst was Dylan on
Andromeda...but pretty much all of them sucked, to varying degrees.
In the non-scifi arena, the character I hate more than any other in the history of TV is George O'Malley from
Grey's Anatomy. Jesus, what wuss this guy is! I mean, a complete and total weenie of ginormous proportions. Not to mention being an incredibly selfish and self-deluded character when it comes to women. Grow up, George! Be a man, fer cryin' out loud!
Runner up in the non-scifi category would probably be Chloe from
24. When she got a second season on that show, I know it was the beginning of the end for me and 24. Whine, whine, whine!
I also really don't like Dexter's sister Debra Morgan on
Dexter. By far my least favorite character on that show. I was actually kinda disappointed that Dexter picked her over Rudy.

Rudy was at least interesting. And not nearly the selfish whiner.
Finally, I don't like the character of Cam on
Bones. She has gotten better as time has gone on, but I really really disliked her alot at first.