I did not expect Koholint to be as popular an answer as it is =O
For me it's the Farewell Hyrule King. It's not even a bitter-sweet goodbye, it's just sad... You can see how much Link wants him to go with them,,, And the music... the music...
I think that, as good as the King's farewell is, LA just built up to its ending more and earned it more. With the King you can really understand his side and empathize with his decision to stay, and even though he's been your support character through the game, he's just one person. Also, it was his decision. Granted, the moment is beautiful and poignant, but also fitting. The vanishing of Koholint on the other hand is basically just tragic. It's an entire world of people and animals you've gotten to know, who all have their own lives and loves, who never asked for any of this, and to do the right thing you have no choice but to wipe them all from existence and simply hope they find a way to continue to exist in some metaphysical way. It's a choice of damnations with no clear Right answer and that no one involved can feel especially proud of. And in the end, all you're left with is a memory and an endless drifting sea...
