At the very beginning, after Cole shows his true and obvious colors, and Byrne cleans the floor with Alphonzo... Link tries to protect Zelda. Even if you haven't gotten the sword, he stands in the way. Byrne dispatches him with an Offhand Backhand, but Link's sheer resolve is awesome in pure form.
The simple fact that Zelda is even accompanying Link on his adventure counts as a Crowning Moment, particularly considering her usual track record.
Zelda, despite being intangible, tries to stop a Phantom from smashing Link — Cue Royal Possession. Which, in itself, is one giant CMoA for Princess Zelda over the course of the whole game. Pretty much every time Zelda hijacks a phantom, Awesome can be reliably expected to follow
Each time Link restores a piece of the Tower of Spirits. There's just something so chilling about the music and sound design in each cutscene, and the fact that the final piece has a more epic rendition of the tune.
Anjean popping up out of nowhere when Byrne is threatening Link and Zelda. A Mentor - Disciple Battle ensues, although it, sadly, happens off-screen (presumably to avoid showing Anjean getting out of her wheel chair. This would have made it necessary to add moveable legs to her model just for that one scene, which would have made it unecessary complicated).
Anjean and Byrne, both wounded, start to argue about which of them should accompany those poor, poor children for the final battle... Along comes Zelda, and she tells them that they don't need help from either of them, because she and Link are awesome enough to take on the Big Bad by themselves.
The final boss fight. Holy crap. It's not enough that Malladus's final form looks suspiciously like Ganon; it's not enough that Zelda's finally got her body back. No, you had to get into a fantastic, Awesome Music-worthy musical collaboration with Zelda and the five Lokomos, which segues perfectly into the final boss theme as Malladus roars and his weak spot is revealed, prompting Zelda to — for the third time since Wind Waker and Twilight Princess — pick up the Bow of Light and fight alongside Link. And the final blow? Link's picked up some tricks from his ancestor — he, with Zelda's help, shoves the Lokomo Sword right into Malladus's forehead. The fact that Zelda actually helps deliver the final blow just drives the awesomeness home.