There were parts in games (as well as the game themselves) that were scary to me in my younger years and definitely even today so I'll go by the top 4 that scared me, spoiler alert
1. Laura Bow- The Dagger of Amon Ra: I'll admit the first murder scene with Dr. Carter in the coffin made my heart pace and I ran out as soon as the next act came. I was 11 around that time. My brother got further and saw Ziggy's head (It's just a head in a black background) and the fake Dr. Carrington's death scene. I didn't touch the game until I played it on my own. The music after the discovery of a corpse was creepy especially the background being black. Those murders in the museum is like adding in the creativity of the kills from the Friday the 13th film with logistics the style of the Final Destination films. Some of the logistics for the kill were just flat out impossible. Even today, I have nightmares of being in the museum.
2. Space Quest 4- the freaking zombie shriek. I first played SQ 4 on PC Speaker, but when we got a sound card, that cyborg zombie shriek was terrifying. I had nightmares of the Super Computer as well before the countdown as well as the zombie. Space Quest 4 is a very dark game in terms of mood and content. I later learned the scene of the zombie pointing and screaming came from the 70's version of Invasion of the Body Snatchers.
3. King's Quest VI: The Realm of the Dead when you first get there with the music and the zombies going about until you get past the guards. The scene where the Lord of the Dead touches you and the death message freaked me out and gave me nightmares after that. Also, when you get locked in for the last time in the cell at the castle was unsettling for me at 10 years old.
4. Shivers- It's been 20 years since I first beat it in the summer time. I always hated it when the music changed to the warning music that an Ixupi is nearby. The most memorable ones were Man Inhumanity's to Man, Strange Inventions, Gods and Religious Items and the Planetarium. The bedroom music as well as the clock tower sounded like something I'd hear in Max Payne 2 with the violin. I never played the second one. Spoiler Alert: I wondered what happened to the Ixupi that killed the students and the professor? Are they still out in the world taking life randomly? You'd think after the museum incident, someone would want to investigate the disappearances and not have to go 15 years later?