Oh god yes, where to begin . . .
I hated Meryl Strife from Trigun for most of the series, particularly earlier on when she got the most screentime. That kind of faded away towards the end, due to the shift in tone the series take & Meryl just getting less screentime and focus. I also hated Kaoru from Rurouni Kenshin for the longest time, probably until halfway through the Kyoto arc. Dorothy Elias-Fahn has a very hateable voice (it's not all the VA's fault though). I hate the entire cast of Rosario + Vampire, but I hate pretty much everything about that show so maybe it shouldn't count. Hate Tenma from School Rumble, she's extremely annoying. Also, Foxy from One Piece. I really, really hate that annoying piece of crap that anime seems to have a hard-on for.
However most of the characters I can think of aren't actually villains that I hate for reasons of them being bad people and the vast majority of the time the characters I dislike are the heroes/protagonist. Mass-murders, totally despicable people with no redeeming qualities, don't really bother me. Just if they're boring, or annoying. A good example of the former is Kano, the big bad of the second half of Texhnolyze. He does probably one of the most fucked up things I've ever seen to a main character and yet that has nothing to do with why I disliked. The only reason I disliked him was because I thought he was boring (hard to imagine they managed making a solipsist boring). Don't hate him though, but he was the first character that entered my mind. So yeah, it's hard to get me to hate a villain.
Also, Rachel from the Dark Knight Trilogy. Nothing worse than a forced love interest who's only real purpose is to be a shoe-in loved interest, doesn't help that neither of the actresses playing her had any chemistry with Bale.