One of the best things about the Metal Gear series is the bosses. Whether it's a girl in a bathing suit who can't be hit by bullets, a cyborg ninja, or a fat guy on roller skates, you can always depend on facing down something completely insane.
Metal Gear Solid 3 is no exception. The core of the enemy brigade is made up of The Cobras, a specialist team that apparently won World War II or something.
My personal favorite would have to be The Pain. Simply because he takes what should by all rights be nothing more than a crippling social handicap and makes it into a strength. I like the idea of a world where the military pays due respect to those individuals with his kind of abilities. I'd love to have seen it: "What are your skills?" "Expert sniper." "Heavy machinery, tanks, and submachine guns." "I'm COVERED IN BEES."
"Oh, and sometimes I do handstands for no reason."