Legend of Zelda: Windwaker - Gannondorf
Lufia 2: Rise of the Sinestrals - Daos, Mastor of Terror
Chrono Trigger - Lavos
Earthbound - Gygas
Paper Mario - Bowser (DOn't know why, but it is)
Star Fox 64 - Whatever the monkey's name was, I forgot it.

But of those that arn't main bosses, Asgard the Divine Fortress of Wild Arms 3. He was awsome, plus a great character.