Naked Snake (Big Boss) - Wins
He invented his own awesome combat techniques with another legendary war hero that he fought and won against with those same techniques. There is nothing that beats that! Except super powers.
The Punisher - Third
I don't know much about him, but there isn't a way he could beat CQC.
Solid Snake - Second
He's an imperfect copy of the Big Boss. That makes Big Boss automatically better. But he still uses CQC, and he's good at it. Just not as good as Big Boss.
Sam Fisher - Last
As far as I can tell, he would only be good if unnoticed until he got the chance to kill people. Not good in a straight up hand-to-hand fight.
Seems like everyone knows how awesome Big Boss is, but they don't know why he's more awesome than anyone other than Solid Snake.
By the way, for people who say that CQC isn't that useful, every single close quarters thing that the Snakes do is CQC, so be quiet. Also, the hand-to-hand combat sequences at the ends of MGSs 3 and 4 prove that CQC is awesome.
Also, Big Boss wins because he can grab people from the front into a choke hold and knock them unconscious, and he's better at it than Solid Snake.