Strangely, I think one of my favourite boss battles ever must be Magus from Chrono Trigger. It happens relatively early in the game as well, I think that's what makes it so epic. You've heard so much about him, they've been building up the encounter since you arrived at his castle, but you still don't know what's he's going to be like to battle against. The fight itself just feels so epic. The music is unique, and his sorcery makes this a tough, but not annoying battle, to have.
The second of my two favourites has major spoiler potential (from Onimusha: Dawn of Dreams):
Another that immediately comes to mind is Richter from SotN. Even though he's not the true final boss, he probably
should have been. He's also quite easy, but that doesn't stop the fight being very climatic in its own way. Sometimes I even play the game fighting him at the end because it's seems like a complete story in its own right.
There are a few others as well, most have already been mentioned. Guildenstern (both forms) - there's something about fighting on the roof of a cathedral that's just so cool!
I'll probably think of some others when I've glanced at my video games list. There are just so many!
Jam it back in, in the dark.