Well, if you're talking about any game, then Dusknoir, from Pokemon Mystery Dungeon 2. He certainly made this game dark, and a lot of the reason why it is one of my favorite pokemon games, and favorite games in general.
He's the commander of Primal Dialga's forces, and is openly wicked in his own time. The fact that he was able to fool everyone, and I mean everyone is a tribute to his own abilities at infiltration. And then he is quite powerful himself, able to fight off Grovyle, the Hero, and the Partner, only beaten by his own attack.
And then we have his ability to make plans on the go. Because I know that plan of Dusknoir's in MD2 Sky wasn't thought of for months, it was on the go, and it was actually pretty good. The unfortunate thing is that he grew a heart, but if not for that, he'd have succeeded.
And even his Heel Face Turn was awesome, and the resulting beating from a weakened Primal Dialga. He's my favorite villain, because they really fleshed him out in Sky, giving him a personality that I like.