My favorite part of OoT is the Forest Temple. The music, the way everything looks, the theme, all of it just makes me slightly uneasy. Not like the outright (attempt at) horror in the Shadow Temple, more like a very subtle feeling of something being amiss. Not to mention I love the puzzles and the boss at the end is possibly the best in the whole game. This makes the Forest Temple not only my favorite moment in OoT, but also my favorite dungeon in the whole series.
I loved so man aspects of Ocarina of Time. I loved fighting Iron Knuckles and Ganon. I also loved the kill scenes for man bosses including Queen Gohman, King Dodongo, Phantom Ganon, Volvagia, Twin Rova, Bonog Bongo, and Ganon.
My favorite scene was probably the part before Link enters the Forest Temple where he encounters Sheik and learns the Minuet of Forest. It was the first scene where Link and Sheik play their instruments together and was a very intimate scene. Also Minuet of Forest is one of my favoriet tunes from the game.
Well overall my favorite part in OoT would be when pull the Master Sword out of the Pedistal of Time. My second part is when King Zora moves away from the entrance to get to Lord Jabu-Jabu...It's the sound that completed that scene.
My favorite moment in the game really isn't a part of the story. I think it's hilarious that if you attack a cucoo too many times (I think about 4) then you'll have chickens flying at you from all over the place!