Really tough choice, but it would have to be as Pikminmaniac said.
The set-up to the fight was incredible with the Triforce reunited, and then the King comes in and uses it himself, thus causing the fabled triangles to disappear.
And it's not only the ocean walls crashing down on you as the fight goes on. It's Ganondorf himself who was pretty epic.
Unlike most games that I've seen and played, where fighting the Big Bad and losing will have him gain something out of him, Ganondorf (with Gerudo Valley gone, the land beneath the sea going to disappear for eternity,
and the Triforce that he sought after for centuries just disappears in front of him, never to be seen again) has
nothing left to lose.
Even if he were to succeed against Link and Zelda, he'll drown beneath the ocean waves. Sure, he didn't transform into a giant monster, but you can tell he was ready to throw his life away if it meant taking you down with him.
And then one of the most epic endings to a video game ever:
It was also my very first Zelda game, and being brought up through an epic journey up to that point was just amazing.