Majora's mask bosses were allot more challenging thats for sure. Gyorg and majora are one of the hardest bosses i faced in any Zelda game. You need to fight majora as normal link rather then Oni-link, hes allot more difficult that way. Its true that they are allot more original and unique, who would have expected a final boss to do moon walks, man that was hilarious. Majoras wrath is a real pain with those whips and spinners and that noise it makes is well freaky, but still Majora is one of my favourite bosses. So i guess majoras mask wins for me.