Reaver, from Fable 1 and 2- Awesome villian, he's utterly horrid and you are meant to hate him. There are no redeeming factors about the guy and everything he says makes you look for the option to whack him in the face. I love him because I hate him.
Cloud- Whiny son of gun, who really should have been told to grow a pair by...well, just about anyone.
Sephiroth- The guy is creepy, not in the bad guy way but in the 'don't touch with a 40ft pole' kin of way. Also, as someone else has said, the guy's dialog sounds like something from slash-fiction.
Yuna, Breath of fire 4- I like a cunning a villain, but not when their smug, karma escaping ass that you don't get to beat the living tar out of. Less about the character more about how it all ended.
N, Pokemon Black/White- Nothing against the guy, but everytime I see related fanart/fanfiction/ fandom of him, I want to curl up and cry.
And finally:
Aeris from FF7- Lots of people I know ask me why, here's the reasoning. A touching deathscene does not excuse a character from being a sickening sweet ball of sunshine without flaws. She was just too nice and sweet, sure you could agrue it's to blanace out the dark world and because she wasn't human. Thing is that still doesn't make me care about her anymore, she was too prefect. Most people might class that as Mary-Sue with a heaping dose of Too-Pure for this World, which doesn't really tug on the heartstrings in the slightest.
Sorry for the rant there.