Mithala's dying cutscene. Most of the other (major) gods just grant a dying "vision" providing backstory. Mithala has a conversation with Naija that will rend your heart. It's comparable to the game-ending sequence, but this is near the beginning of the game.
That said, the game-ending sequence is pretty moving too. (See also Cry for the Devil under YMMV.)
Crowning Music of Awesome: Considering that the main character's sole method of attack, defense, and puzzle solving is through singing and that this power is called "The Verse," it really comes as no surprise that the entire soundtrack qualifies for this. Bit-Blot put a lot of heart and effort into making the soundtrack for this game memorable, and made sure that you'd be listening to every bit of it as you wander the ocean. And that refrain you've been listening to for the whole game turns out to be the key to a late-game door.