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.)
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.
The mere fact that, despite having little knowledge of the world and starting out as nothing more than a creature slightly more powerful than a fish, Naija ends up taking on and defeating Gods and insane creatures. She's faced Ghosts, the Sun God, Mother Nature, the God of a warrior race, and much, much more all while simply trying to learn about the world. She was never determined to kill Gods and spirits, she simply beat them because they were there.
Which makes the Eleventh Hour Super Power even better. The Creator had gone too far; he took the one person Naija could ever call a friend and companion, and his connection to the deaths of many civilizations has struck home. Now she is determined, and the Dual Form lets her unleash her full rage.