Most of the anime I watch doesn't tend to have "villains" in the normally accepted meaning of the term.
One that does come to mind is Nakago from Fushgi Yugi, the most powerful member and leader of the Seiryu Seven. He's on a personal vendetta to extract revenge on just about everyone for how his tribe was treated and he'll use anyone to achieve his aims, and callously dispose of them when they're of no further use to him. He is, in short, a thoroughly nasty person.