I have 3 answers. I played all those 3 games on my Amiga 500 Plus.
Prince of Persia. Lack of music is already creating an eerie atmosphere. But that screaming sound the main character makes when he falls down to his death traumatized me. And also the gore, of course.
Clive Barker’s Nightbreed: The Interactive Movie. Thank you, my ignorant parents, for making me play something labeled “Clive Barker” as a kid.
Qwak. The game is super cute but, those falling spikes!
What are yours?
Silent hill 1 without a doubt, even the music still makes me scared and unable to sleep at night when I hear it 
Phantasmagoria. My parents didn’t know how messed up the game is and to this day I still didn’t see what happens when the demon catches the protagonist. My brother told me her face gets ripped apart but I always covered my eyes so I wouldn’t be traumatized.
Face ripping was probably the most tame thing in that game for a kid to witness.
We had a demo for Alone in the Dark on PC. It totally creeped me out when one of the monsters was coming up from the floor all slowly and the music was scary.
The zombies in the water in Quake were pretty creepy.
I was a teen, but–Fatal Frame 2. I fought the Falling Woman and thought she wouldn’t show up again. Then I backtracked through her hall. She screamed and fell out of the ceiling, I screamed and dropped my controller, and the two cats keeping me company went flying off the couch and fled for quieter pastures.
I mean, there’s a lot of disturbing stuff in that game–the Woman in Box, aka the Sadako tribute, still creeps me out–but FW’s surprise second appearance OUT of the ceiling nearly had me jumping INTO the ceiling!
Unfortunately, I don’t know the name of the game, but I remember playing a room escape game online when I was a kid, that was realistic and horror-themed(an abandoned place, I think).
In one of the rooms, I saw a vent. I clicked on it which changed the point of view so the whole screen was the vent. Nothing happened when I opened it, but I could hear a sound. And a weird disfigured human came running out of it. I freaked out so much I screamed. I went to my older brother, who was in the same room and saw me jump, and stayed away from the computer for a while.
I haven’t played any creepy room escape games since and I will never play a horror game with jump scares.
Illusion of Gaia. Not practically, but conceptually. There are some heavy themes in that game that were pretty disturbing and the game used atmosphere to heighten the experience of those themes. There were no traditional scares, per se, but overall it was a very creepy and unsettling game.
I had the same experience with a room escape horror game! I used to love room escape games until I accidentally started playing one with a creepy theme, and now anytime I try to start one my paranoia ramps up, lol.
The original Resident Evil and Silent Hill 2.
Playing RE with my cousins after lunch on family reunions was the stupidest decision we loved to constantly make.
The original resident evil PS1 games. And that hasn’t changed 
That damn werewolf from Ecstatica. Everytime it appeared I panicked and died. There is no happy ending to the story, I didn’t see much of the game.
Agreed, Resident Evil was scary the first time I played it. But I was obsessed with that game, so I played and replayed it until it lost its power to scare me. The clever thing Capcom did with Resident Evil was remixing the game for the HD remake. When every cues you expect are suddenly gone, or have shifted locations, you suddenly feel quite helpless all over again.
Resident Evil as a series has a tendency to grant you too many weapons during the second half of every game. I just finished a run through Resident Evil 7, and while I was terrified during the first half I felt like an invincible bad ass during the second. Parto f me loves that because I’m not scared anymore. But part of me wishes they’d keep the stakes high throughout.
I envy you, I get scared easily and most movies and games are too brutal for me. The closest thing to horror I played was Devil May Cry 1. It was a bit disturbing but the most scary part was difficulty 
I haven’t finished it 
I hate Marionettes, they remind me of clowns.
I thought of another! Another World! That thing that chases you in the early part of the game! Aghhhhh!
Yes, the leaches/worms creeped me out too.
A bunch of CD-ROMs terrified me as a child.
The Assassin Droids in Star Wars: DroidWorks. The game is such a solitary and challenging (for a child) experience and then they throw in these lethal sods to chase you down whilst jeering. I’ve never jumped more out of my skin.
This thing in The Pink Panther: Hokus Pokus Pink. It’s bizarre enough throughout, but this was too much.
Maniac Mansion and the Kemco point and click games.
When Nurse Edna chases after you, ugh.
Shadowgate was creepy in general but mostly okay, but Uninvited wrecked me. The hallway ghost woman mainly. I had to sleep in my parents’ bed that night.
Oh, and how could I forget Moonstone??? Intro was very creepy and mysterious. As far as I can remember, enemies could kill you instantaneously and that was keeping me on my toes. That dragon boss was so big that you could only see its head! Killing it felt incredible though. And of course, the gore…
Dino Crisis. Hell that game made me cry inside when I was a kid. I always saw my older cousin playing it. Never got to play it all by myself. Maybe I will someday. Maybe if they ever make a remake /remaster.
To be honest it is a bit hard to think of a game from my childhood that fits the criteria.
I am trying not to be cliche and draw upon creepy pastas but the closest thing I can think of was not so much a game but the entire scenario of being in Lavender Town, which made me feel uncomfortable as a kid when the game first game out, and sad as an older player.
Another instance that I can think on, and this can be attributed mostly to the score if you can even call it that would be the dungeon theme in A Like to The Past. When you enter the first palace, the music carries this ominous and slightly unnerving and erratic intrusion. I feel like it really sets the stage for the journey you are about to embark on within any of the particular dungeons throughout the game.
Again, these aren’t the whole games but merely sections that I remember.
~ Prin
I played Resident Evil 2 for the first time when I was 9 and I was home alone during the day. Couldn’t make it past the title screen because it bothered me so much.
I had to make my mom sit with me through the hospital area on the first Silent Hill. The nurses still freak me out with their erratic movements.
But the first one to really have an effect on me? Either the original Mechwarrior or Another World. Mechwarrior’s game over screen, with a face gasping out from the darkness, still haunts me. Another World got to me because of the leeches. I’d never heard of parasites until I played that game, and once I learned what they were I developed a lifelong phobia of parasites.
