Contra - Red Falcon's Heart: Destroy the four pods, and he's helpless.

King of Fighters 2001 - Original Zero and Igniz: CHEAP, CHEAP, CHEEEEEAP!!!

FFX - (can't spoil): If you could slay Nemesis, you can surely kill this guy in TWO moves.

Time Soldiers - Gylend: After the actual stage itself, (and those damn eye-plants) he's a slice of pie.

The Genji and the Heike Clans - Minamoto Yoritomo: You have the three magic items, and he is so screwed.

Ghosts 'N Goblins - Lucifer: What an anticlimax to such an otherwise machine-wrecking game.

And THE big one...

Gradius - Bacterion (?): The ultimatum of disappointing bosses!