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.
The end credits, without a doubt. Everyone Lives. Your uncle, the king, 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 Crowning Music of Awesome.
Sahasarahla'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 Dark World 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 Game Boy Advance version, in which Link brings peace back to the not-so-bad Dark World. The animals are no longer vicious and trap Ganon's minions as they dance around living naturally, the thieves in Thieves' are Town 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.