Interestingly, the enemy that scared me most was OoT Redeads. The artwork of them in particular creeped me out.
I would get so nervous when getting the Sun's Song, or going into the Bottom of the Well. I went out of my way to beat the Spirit Temple without the Lens of Truth or the Hover Boots (it's possible, but difficult) in order to save the Shadow Temple and well for last. I had to really work up the nerve to beat the game the first time, because I kept running out of those levels screaming with my heart racing. It was like a horror movie for me.
The first thing I ever wrote and had published online is actually me asking someone how to get over my fear of them on a site called HTLOZ that was popular back in the day. There's still a record of it, apparently.
http://www.htloz.net/archives/htloz/1999-08/letters.html
I think I first got Internet access in December 1998, so this was just under a year after I got online for the first time. He probably thought I was trolling him, but I was actually serious.
I get ReDeads, I'm replaying through Oot rn and those things still f*** me up.ReDeads!
There I was in the graveyard pulling back a stone and I discovered a hole in the ground. Of course I went down to see what was down the hole and once I had entered I saw a naked brown man. So I went over to investigate but then I heard this horrible scream. Next thing I know he was on my back, molesting me. I tapped my controller frantically trying to get free but there was nothing I could do. I had been buggered to death.
I had nightmares for years about those creatures and I was terrified to approach them in game from then on.
LikeLikes
These were almost as scary as the ReDeads. Now I know it's not a huge deal if you get your shield or tunic eaten, it is just an inconvenience. However for a young me having my shield or tunic eaten was THE END. If I got sucked up I would switch my console off at the mains. The sound of the LikeLikes made my heart race. My worst encounter with them was in MM because there are hundreds on the beach at night and I really wasn't expecting that.
Wall/Floormasters
The wallmasters shadow above me made me want to wee myself and like @Satan said being taken back to the beginning of a corridor seemed like the worst thing ever.
The floormaster was also scary. Like the ReDead and LikeLike these enemies can grab you and I don't like that feeling of helplessness as I am in their grasp.
Takkuri
Having your items stolen was even worse than death especially if you didn't know how to get them back. The Takkuri was as bad as the LikeLike in this regard and plus it looks creepy.
I get ReDeads, I'm replaying through Oot rn and those things still f*** me up.
The well in general like @Shroom said, still have to mentally prepare myself for that. As a kid I went into the well think "Yes some sort of water dungeon" I go in there and I didn't touch the game until much later in the week. That's how terrified I was back then and still am.
The puppets in the Lost Woods in TP, not sure the actual name. Those things are outright creepy and every time I went in there I dreaded the chasing Skull Kid around having those things pop up randomly. One time I was using the Hawk Eyes looking around my first time up at the trees cause I though I say something and one of those magically appears; me *screeches resembling a banshee dying at the hands of a redead while falling of a high chair while crossed legged*
And honestly I don't get why people are afraid of like-likes
Oh and the 4 Pod souls in Arbiter's Grounds. Arbiter Grounds in general I get scared way to easily