If I listed them top five, one being most scary....
5. Meeting Guru-Guru in the windmill for the first time. Loved the music... the man, not so much.
4. Being abducted by a wallmaster for the first time.
3. The Bottom of the Well....enough said.
2. The Forest Temple( the music scared me the most and it felt like I would get lost there. Also felt as if I was being followed...)
1. The graveyard behind Kakriko. When me and my friend first discovered it I didn't want to play. I handed over the controls to him. First the ghost comes out when you play the song. Then the first chamber underground is full of bats and skulls and bones. Then you come to the room with toxic green goo accompanied by a bunch of living mummies that scared the crap out of me. I refused to play. Then the final room really scared me. Remind you my friend is still playing. I thought as he walked to the alter, something would pop out and kill him.( This was when I was 7 but even now it still freaks me out. I have to remind myself it is just a game and I can retry from last save
)
Most of my moments are from Ocarina just because it was the first one I played when I was younger. This made it easier to scare me.