Metroid Prime 2 - Mutated Emperor Ing/Dark Samus (both of them are awesome)

Metroid II - Metroid Queen (love that song, it sounds kinda evilll, and bombing that stupid thing's stomach is the best thing ever)

Super Metroid - Mother Brain (It's a sad moment, and I love pwning her via Hyper Beam)

Final Fantasy - Chaos (I've always found it fun, for some odd reason)

Final Fantasy VI - Kefka (Hands down... the best)

Final Fantasy X - Yu Yevon (way too easy, but the music is again catchy)