tambourine
Banned
Final Fantasy VI's Kefka
Half-Life's creepy G-Man
Full Throttle's Adrian Ripburger (voiced by Mark Hamill)
The Legend of Zelda's Ganondorf
Starcraft's Sarah Kerrigan
Mike Tyson in Punch-Out!
Command & Conquer's Kane
Along with many, many more that escape me at the moment...
Personally, I'll rarely ever enjoy corny villains like Bowser. For certain genres like RPGs and adventure games, they can be the game's biggest attraction, or at least the best character. It's like, you're motivated to go on and bear many trials and frustrating hours in front of a screen, only to confront your nemesis.