One that really jumps to mind is Alex Vance from the Half-Life series. For all intents and purposes, she's an alright character...but the way she's so forcefully friendly with Gordon sickens me. Most of the time, when stuff is happening, she's cool, but it's whenever you're splitting the group up or in a non-combat situation that she makes me squirm uncomfortably. I just don't see any reason for her to act the way she does. With that said, Half-Life is still one of my favorite game series. I'm a sucker for singleplayer first-person shooters with minor RPG elements incorporated.
I have no idea if anyone actually liked them, but the two female characters from Dark Messiah: Might and Magic made me ragequit about 10 hours into the game. I seriously got so sick of those two dimwits. Xana and...Leana? Don't remember. Either way, they ruined the game for me. Forced companionship/romance is something that can instantly make me dislike a game, depending on the character(s) in question, and neither of these two fit the bill of being acceptable. It didn't help that Xana's voice actor AND dialogue were...not very good, either.
Ashley and Liara in Mass Effect 1 sickened me as well. Forced romances...*shudder* I didn't even talk to Ashley once and she still automatically assumed that I was romancing her! Absolutely dreadful. Also, Miranda was one of the most hideous attempts at making a character "beautiful" that I've seen. What a terrifying face.
Baldur's Gate 2, even though it's one of my favorite games, also falls prey to idiotic BioWare's idea of romances - you talk to a character once or twice, and they're automatically in love with you! Ridiculous. It, however, gets a pass, because I liked most, (actually, mostly all) of the characters.
(edit) Also, all the characters from Dragon Age: Origins. I don't think I liked a single one beyond Duncan, who dies right away anyhow. Shale was alright, too, I guess.