For the first time in a Zelda game, Hijacked by Ganon is inverted by Yuga, who despite transforming into a monster similar to Ganon, is in complete control and still manages to be the Big Bad.
In the final battle, the last Light Arrow that you fire. The others were achieved by firing at Yuga, exiting the wall, and firing at his back while he was occupied. The last one? You fire it away from him and it travels all the way around the wall to finally hit him, the room darkening around it and the camera following it.
Forthefifthtime ever, the Triforce is actually used! And it has enough power to recreate another Triforce of equal power!
Ravio's moment at the end of the game. He finally decides that enough is enough and jumps in to talk some sense into Hilda before any more violence comes to pass. It just goes to show that even the most cowardly Link has some courage in him.