Seiously, I know Nintendo games aren't all that scary, but when are some times you were truly frightened in a Zelda or Mario game? Maybe a weird creepy boss or enemy or just something unsettling. I remember a room in Wind Waker: Tower of the Gods where there were two Armos Knights that I thought were just decoration. Then I made a chest appear and opened it and they came to life. I had no idea how to beat them. They were just chasing me around very quickly and I thought I would die.
I remember being real scared of Phanto back in the day. One reason I was reluctant to ever continue SMB2 (the SMAS version). I hated 1-3 because of the long vertical segment and having to item babysit the key. I did not think of dropping the key to make Phanto go away, just had to get away real fast. The Phanto statue in the BG with the glowing red eyes in the room with the key did not help at all.
Legacy custom music
A site with a non-useless dislike button
SMW hacking channel