Shadow - Final Fantasy VI. Mysterious warrior. Not a big talker, but was there when most needed.
Well, except for when he'd up and abandon your party right after a battle.
And I just thought to add some more favorite villains (?).
Sydney from Vagrant Story. Enigmatic and powerful enough to compensate for the overwhelming androgyny, what really sealed his awesomeness was the realization that
he's actually a hero martyr grooming a successor. The very fact that the power of Lea Monde only served those who did not desire the power proved that he had been living under a great burden the entire time he shouldered his responsibility.
And of course Yuber from the first three Suikodens. As far as I'm concerned, Suikoden stopped being Suikoden when they took out that common thread and escalating conflict of the mysterious black dude who radiated scary danger, Will Robinson.
The dude was dangerous enough that your party flat out says they don't stand a chance just by looking at him when you meet him in the first game. The fact he plays second fiddle to the antagonists is overshadowed by the fact he plays second fiddle to ALL the antagonists, for over a century, and could probably devour them alive if he wanted to, despite helping them achieve their relatively petty goals.