The bosses of Fallout 1 and Fallout 2 are pretty cool ideas. (And as you kill them they have special death animations that are very gory and satisfying)
The bosses of Super Smash TV are awesome and quite memorable (and they scream and moan and taunt you as you shoot 'em up)
The boss of Duke Nukem 3D has a satisfying and hilarious end.
This guy. not a boss per say but probably the scariest enemy in a game 
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