Flammie! Best boss battle ever! Or at least one of the best boss battles ever.
The whole SoM final boss sequence is awesome, from Fanha onwards, but Thanatos and Flammie in particular are truly incredible fights. The fight against Flammie is so awesome not only because it, of necessity, lasts for a long time, but, even more so, because of how it fits into the story: The premise is that the Mana Beast will destroy the world by flying into the Mana Fortress, which is a difficult premise to execute graphically, but they did it fairly well, and the idea itself of the world ending because something crashed into something else is so compelling that I adapted the idea for use in my own novel.