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.
After Yuga-Ganon absorbs Hilda, he stands there laughing and gloating as two-thirds of the completed Triforce glows within him. Link glares at him and defiantly raises his fist, showing the Triforce of Courage as if to say, "You don't have the whole thing yet! You want this last piece? Come and get it!"
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!
Link charging into Hyrule Castle at the end of the game's first half, as the Master Sword effortlessly slashes through any enemy Yuga can throw at him as he's forced to retreat to the top.
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.
Have fun fighting the Streetpass Shadow Links that Gramps sets up for you? Well, complete all the Challenges and you get to fight Gramps himself, who's carrying a fully upgraded Master Sword, Tunic and Shield, as well as two random upgraded items, and matches your attacks with his own. Winning means you're not just good enough to defeat the remnants of other players, but also able to essentially defeat yourself in single combat.