By "ugly", do you mean 1) grotesque (i.e. any Resident Evil boss), 2) a character who would be considered ugly in real life, or 3) a character whose graphics are ugly, regardless of whether the character themselves would be considered ugly?
I'm going to assume 3, since I happen to be rather fond of grotesquerie, and I'm not into judging people's looks on the internet (even fictional ones).
As far as characters with ugly graphics go, I think anything from the original Alone In The Dark would qualify, but the special prize has to go to Emily. The character herself looks fine, but thanks to a low poly count, her in-game model has a tendency from some angles to suddenly go wall-eyed, develops a massive jutting brow, and her lips stretch wider than her face. The result is a graphical horror that an Innsmouth hybrid would run from screaming.