* In spite of the various signs posted in Hyrule, the vast majority of people in Hyrule still treat Link as they always have with the snitches being in the minority.
* A first time player may (justifiably so) mistake Agahnim's line "Behold! The last moment of Princess Zelda!" before sending her to the Dark World as killing her, but then the player gets a telepathic message from her in the first dungeon.
* Finally, ''finally'' recovering the last crystal from the dungeons, and being reunited once again with Princess Zelda, who is so glad to see you.
* The end credits, without a doubt. EverybodyLives. Your uncle, the king, the Sanctuary Keeper, the Flute Boy (or is it Ocarina?) and his father. And though the ending doesn't show it, the old man on the mountain undoubtedly reunited with his granddaughter. All set to SugarWiki/AwesomeMusic.
** Sahasrahla's homecoming: You see the elder who hides from evil throughout the game with his wife and grandson, and before this you never knew.
** The camera sweeps down and shows the two brothers who were so mad they sealed up the doors to their rooms, happily together.
** The bird that was trapped in the statue flies happily around where it was.
** The Bully makes a Friend: The fickle boy who turned into a ball in the DarkWorld and kept on being bullied by the short tempered person who turned into an ogre? [=BFFs=] who play Tag.
** Your Uncle Recovers: He dies in the beginning of the game before passing his sword, shield and legacy on to you. Self explanatory.
** The bug catching kid has happily recovered from his disease and got his favorite Net back.
** Overall one of the best endings that shows what the Hero has done by bringing peace to Hyrule.
* The extra ending from the UsefulNotes/GameBoyAdvance version, in which Link brings peace back to the not-so-bad Dark World. The animals are no longer [[EverythingTryingToKillYou vicious]] and trap Ganon's minions as they dance around living naturally, the thieves in Thieves' Town are sharing loot, the money-loving Monkey is juggling his cash happily, the lion-like enemies rule Death Mountain and the Cyclops are playing catch with bombs.
* In a roundabout way, the Hero of Time gets a second chance at defeating Ganon, since every Link is a reincarnation, and it was the Hero of Time's death which allowed the events of this game to happen.