It's not exactly a bold choice, but I'm going to have to go with Ganondorf/Ganon from OoT. So rarely have I seen a boss fight where story, music, gameplay, and atmosphere could be implemented in such mutually beneficial ways. You're fighting a man hellbent on obtaining true power; even the suspense of climbing the stairs to get to him is impressive (they certainly seemed to draw it out
). An ominous, eerie feeling as the music presses forward, that really gives captures the emotions of the encounter.
Then, after some of the most impressive cutscenes of its time (that are still impressive today), after the toppling of the building, it's pitch black in darkness. After the smoke clears, you're surrounded only by a sea of flames, with a lumbering, looming colossus creeping towards you; you can only catch the occasional glimpse of it as lightning and thunder briefly illuminate the battlefield.
Astronomically beautiful and epic, something that I will never, ever forget.