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Video Games That Had Scary or Unsettling Music

The "music" of the Upper Cathedral in Bloodborne, where it's basically a single women singing, is very eerie, especially when coupled with the overall atmosphere of the place.

Good recent example. Music is used sparingly in these games, and the Upper Cathedral Ward theme is really effective. (The singing you mentioned comes in half-way.)

The theme for Yahar'Gul, Unseen Village is also really spooky. The "angry" chorus and deep bass at the very end of the track gets me every time while playing...

Also, before I even knew what Ludwig looked like, his boss theme terrified me.
That brass is just so powerful and unsettling. And the strings that follow add a hint of sadness. Maybe it's partially the cutscene that leads into this part of the music, but it all works together so perfectly.
He and that music will be stuck in my mind for a long time.
 
For me it would be the entire ambient soundtrack of Stalker: Shadow of Chernobyl. Still my favourite horror game of all time.

It would send shivers down my spine while I played, especially when everything was quiet, making your trek to delve into one of the underground labs and being down there... its a masterpiece.

This ambient track is my favourite of them all, it's stunning.
Also this part in one of the ambient tracks.

Also the menu theme... it just captures everything about the game - the melancholic atmosphere (plays till about 2m5s point)
 
I mean, I guess this kinda goes without saying, but Alien: Isolation.

The music in particular, when it ramped up, was terrifying. You knew you were under serious threat in the game.
 
Moar RE gushing

Reisdent Evil 1 - Big Big Spider

Resident Evil 1 - Lab Enterance

Resident Evil 1 - Lab B3

Resident Evil 0 - Training Facility Main Hall

Resident Evil 2 - Mr. X

Resident Evil 4 - Ganado III

Resident Evil 4 - Regenerator

Then Silent Hill 3, Hilltop Center Nightmare Ambience. The demo here was my first foray into the series and my 13-yo self didn't take it very well

More from non-horror games

Final Fantasy VII - Those Chosen by the Planet (Sephiroth's Theme)

Xenogears - Omen

Resedent Evil 5 - Majini III (They used this in a trailer and it fooled me into thinking the game might actually be scary in parts)
 
Not me personally, but the theme music from the Amiga version of Flashback still gives my Brother nightmares and he's 26.
 
Übermatik;199641486 said:
Unsettling? Hm, Forest Temple springs to mind...

https://www.youtube.com/watch?v=hmsZyC0UXUU&spfreload=10

Though admittedly it's not scary, more creepy and haunting. This combined with the atmosphere had me walking cautiously... Shadows of falling hands, false ceilings, magic paintings...

Arbiter's Grounds too: https://www.youtube.com/watch?v=2gCtO5dr3o8&spfreload=10
That original 'screech' put me on edge a bit.

Yeah that Forest Temple was quite the mood shift

Both of LttP's dungeon themes are a bit creppy too
 
The 999 soundtrack :0

Also, Magus' Castle

This is way too far down for Chrono Trigger. That game had some of the most haunting and unsettling music of all time. Literally so many I would be hard pressed to list them all. I will do my best to list the relevant entries; please forgive me if I miss any.

Memories of Green

A Strange Happening

Kingdom Trial

Lavos' Theme

Battle with Magus

Zeal Palace

Schala's Theme

All of these are outstanding tracks. I can safely count them as haunting, at least anecdotally, as they still have the ability to give me chills after all these years. The feeling of foreboding that this music can create is nearly unparalleled.

Honorable mention.
 
The elevator music in Metroid always creeped me out. Sounds like someone just pressing numbers on a phone, but there was something unsettling about it.
 
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