* The death of Link's Uncle at the beginning of the game --
--> '''Link's Uncle:''' Link... you must rescue Princess Zelda. Our people are fated to do so. But do not fall victim... to fate... Link...
-->''I shall always remember... our time... together...''
** It needs to be pointed out that he does get better in the ending, but you are challenged to say you knew that the first time you saw him like that.
* The Flute Boy scene. He can't play his flute anymore and asks Link to play it for him. Then he turns into a tree.
--> "I just wish I could have seen him... one more time."
* The [[http://www.youtube.com/watch?v=LJh3D_zX0To credits music]]. [[UpToEleven Holy shit]], that credits music.
* The scene that plays if you return to the Sanctuary after getting the Master Sword. [[spoiler: 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 [[TheBadGuyWins 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.