An unexpected one happens near the end, where Bellum grabs Link and Tetra, ensuring the hero's defeat, until Linebeck picks up the Phantom Sword and manages to free them, at the cost of getting himself possessed.
The Cubus Sisters have one right before you fight them.
When Link finally gets the Phantom Sword, the cutscene starts as a CMOF, but then... the energy coalesces into a blazing white sword-shape on a black background, only Link and Oshus in full-color. Link grabs the sword, swings it a few times, then gives a stronger swing — and the white leaves the sword, turning the background pure white and leaving the sword colored.
Pretty much everything after you enter Bellum's lair is a crowning moment of something, and a lot of it is pretty awesome. One particularly epic example is when Tetra is snatched away by Bellum, who then merges into the ghost ship. Linebeck's reaction is to instruct Link to man the cannon, before taking the wheel himself and chasing after the possessed ghost ship. Complete with a particularly epic remix of the game's main themes as Crowning Music of Awesome.