Giygas' Battle [http://www.youtube.com/watch?v=ZUM8p1SdB3k] was pretty badass for its time. As was his true form's theme [http://www.youtube.com/watch?v=p8ZubcNyUPY&feature=related].
I've always enjoyed Yami [http://www.youtube.com/watch?v=sfjeofPxal8] and Ninetails' [http://www.youtube.com/watch?v=rdMFVSR7oNg] theme from Okami, as well.
Then there's Tabuu [http://www.youtube.com/watch?v=R0PvTo9Dkt0].
Also, your sworn rival in his last battle [http://www.youtube.com/watch?v=JhfJO366AM4]. You've been fighting since you were children, you know... Same goes for these ancient [http://www.youtube.com/watch?v=GSYUacOWP8w] creatures [http://www.youtube.com/watch?v=-9rilh2ibGM].
Also, the Sixteenth Colossus [http://www.youtube.com/watch?v=rxZtlk0fdwY] has a pretty good theme. It's a lot deeper and more somber than your standard final boss adrenaline rush music.
This one [http://www.youtube.com/watch?v=X4kpNDJjZxc&feature=related] goes without saying.
And finally, while not really a boss, no one can hear this [http://www.youtube.com/watch?v=U8SZFOeFE0Q] play without at least thinking "Oh, shit..."