i dont wanna repeat too many of the same things everyone else has listed but i didnt get to read every post. here are some of my favorite moments:
-Shadow Link battle (Zelda II). I just barely surived the fight with the Thunder Bird and expected the game to be over only to go on and have to fight shadow link
-Jumping over Geradu Canyon on Epona
-Diving into the water off of Geradu Canyon, seeing link hold his arms at his sides and the way the camera pulls back. the fall is so deep, i always get a chill because im kind of afraid of heights and it honestly makes me feel sick in the stomach cuz i know i would never have the guts to jump off a cliff that high.
-Links eyes when he stares into the empowered master sword right before the final blow to Ganon
-Watching the Tower of the Gods rise out of the Great Ocean and everything that followed (completing the dungeon, being sent underwater, etc)
-Replaying WW and understanding the Hylian Text. Lord Jaboon asking the King of Red Lions if Link was the same Hero as the Hero of time was great
- Thinking Turtle Rock dungeon was the last dungeon in ALTTP and finding out Ganon wasnt in the boss room
-Wondering about the first Deku you see in MM (when you're chasing Skull Kid) and then finding out it was the Butlers son at the end of the game.
-Sniping a poe from long distances on horseback in hyrule field.
-the "alien invasion" in MM
-the "milk heist" in MM
- Playing the Ballad of the Windfish in the Milk Bar in MM (because it brought back great memories of LA after losing my copy

)
-Seeing a giant Moblin for the first time in OOT
-Breaking out of prison in Geradu Valley and sniping as many warriors from the window as i could with my bow
- Playing Zelda II for the first time and realizing Links up/down thrust moves from Smash Bros. (as well as great temple level and music) were from that game.
- Wondering what Nabaroo meant when she said "if i would have known you'd grow to be such a handsome man i would of kept that promise i made to you then" (nintendo innuendo ftw)
- Every time i turn on ALTTP; the chime given off when it says nintendo, the music as the triforce is falling into place, then the sound of the sword as it appears behind the Z in Zelda as the epic music plays.
-Getting the bottle from the salesmen in Kakiriko Village in ALTTP and him saying "now hold it up above your head for the world to see, its good for business." i laughed so hard the first time i read that. its the only time i can think of where the series poked fun at itself.
-noticing the carving on links (tree)house of him fighting a giant monster with a fairy at his side
-shooting an arrow into the sun..
-hearing that classic zelda tune get louder and louder as you climb the steps in Ganons Tower right before you reach the door and see Gannondorf playing the organ. Brilliant how they worked it from behing background music to an actual part of the games story.
-the scene following the previous moment, when the camera pulls out and shows gannondorf, zelda and link in the same positions of the triforce that each represents.
phew i could go on and on but i think my list is big enough