Encountering the Gibdos in OoT MQ. They were in the bottom of the well, and when I opened the door to the room with lots of coffins, a Gibdo was right in front of me! He was so close that I could slash him with the Kokiri sword. But I was frozen before I could do anything. He made me want to leave the room immediately. That was the first time I've ever met a Gibdo (I played OoT MQ before the original one), and it scared me to death. Even now it's still creepy...
Another creepy moment is fighting Dead Hand in OoT. I remember when tha hand caught me, I screamed so loud me that my mom thought something happened to me and burst into my room. -_-'