Fighting against Hitler and his Spear of Destiny in <i>Persona 2: Innocent Sin</i> was pretty interesting. Best part, of course, was beating him and challenging the real enemy, who was made up of body parts of the fathers of the main party members.
Anyone here play kingdom hearts? I loved the game, the end boss could have been more epic and some how better... dont really know how... but the 33 fights before him were great, it was just the getting your friends back in the dark rooms that let things down.
If you bothered to read the previous replies to this thread you would have discovered that SquirrelKnight and I think a few others mentioned Kingdom Hearts.