The Metal Gear Solid bosses are great, because not only is the combat interesting, but then there's usually some sad back story that will make you

right after murdering them.
Thoughts:
Liquid Snake - Brute force fighting. Two shirtless men punching each other like a Van Damme film. Manly.
Revolver Ocelot - Fun, although super easy on the GameCube. Plus, the guy doesn't shut up!
Sniper Wolf - Very Fun, especially with rockets. Poor Otacon.
Psycho Mantis - Super insane!
Vulcan Raven - The tank's kind of annoying, but the railgun teaches you fear!
Hind D - Man vs. machine.
Solidus Snake - Swords, but annoying. Takes far too long to kill this guy.
Vamp - Annoying until you get the pattern down.
Fatman - Ranges from annoying to a great time killer.
Fortune - A boss that can't be defeated!!
Olga Gurlukovich - A whatever kind of fight, but playing MGS2 again recently made me realize those random cinema breaks during the battle foreshadow her latter affection for Sunny. Irony!
Harrier II - Just like the Hind D, but on speed.
The Boss - Wildly fun.
The End - LEGENDARY!!!!
The Fear - I hate fighting this guy. Even with thermals.
The Fury - Like fighting Vulcan, but I like the guy. Plus, he was pretty much the only Cobra with a back story.
The Pain - WTF? Bees? Sometimes MGS can be weird.
The Sorrow - A boss where you're supposed to die!
Colonel Volgin - The best part about fighting him is putting on the Raikov outfit.
Young Ocelot - Ocelot is rarely a challenging boss.