Please, try to post why they annoy you. Oh, and Pikastar7, just to let you know, Code Lyoko isn't anime. But still, I can see why it's easy to get confused. ^_^ (and Mimori, I thought you liked Yugi. *confused* Guess you changed your mind.)
Anyhow...my list isn't going to be too long. (I apologize to any fans of these people. Everyone can have their own opinions about this)
Pokemon
Brock: He's just getting so boring. And the whole thing about going after girls is getting REALLY old. Does he even do anything anymore?
Team Rocket: I don't hate them. It's just that they show up in EVERY SINGLE EPISODE. It's getting so old. And they're just REALLY annoying after a while.
Several filler characters: Various reasons.
Yu-Gi-Oh
Tristan: Annoying as heck. He doesn't do anything, and he's an idiot.
Kaiba: He's just so damn stubborn. He refuses to believe in magic and stuff even when he's experienced it for himself several times. And he's such a jerk! I mean, I understand that he had a rough past and all, but still!
Rebecca: Don't get me wrong, I don't hate her. She just bugs me sometimes.
Weevil and Rex: More Weevil than Rex, though. They're really irritating, but they make great comic relief.
Vivian: Thank God she was only there for that one tiny season. SHE WAS SO EVIL!!!!! 0_o
Megaman (even though it's not showing at the moment...)
Not many for this show. Just....what's his name....Dex, that was it. He hadn't appeared much in the newer episodes, but he's just so...I dunno, just something about him bugged me.
Yu-Gi-Oh GX
Jaden: UGH!!! He's such an idiot sometimes! And what's with all those stupid expressions he uses?
Dr. Crowler: Do I even need to explain? 0_o
Along with several of the random one-time characters. *coughdemitricough*
Let's see....that's about all I can think of at the moment. (I've said it before, I'll say it again: I don't watch much anime. There's plenty I'd like to see, but don't get the chance.)