I'd have to say Link from Twilight Princess. He's the silent dungeon roaming, monster killing hero! And despite the fact that his outer appearance looks like a adolescent female...He's still cool in my books.
I also think Old Snake from MGS4 is awesome. His aged look gives him character and he still kicks butt even though it looks like alzheimer's is about to set in at any moment lol. I still think he should of gotten a girl at the end of the game. Just seems like that type of hero.
