The scene that plays if you return to the Sanctuary after getting the Master Sword. There, Link finds the Sanctuary ransacked, with Zelda kidnapped to be used as a sacrifice by Agahnhim, and the Sanctuary Keeper fatally wounded.
The comic book adaptation's ending. Link saves the day, kills Ganon and wins Zelda's heart... but they can never be together because he has to guard the Triforce forever, all alone.
Ephemerelda crying as she says goodbye to Link.
The fact that this is is the first game in the official timeline that takes place in the era where the Hero of Time is defeated by Ganon. The weight of this game becomes a lot more harrowing when you realize the most iconic incarnation of the hero's legacy had to lose in order for it to happen.