The Sonic Youth track that's always creeped me out the most is "Providence." The static, the ghostly piano, and the muffled voice of Mike Watt in the background.
Ween - "Spinal Meningitis" Why they wanna see my spine, Mommy? Why they wanna see my spine? It's gonna hurt again, Mommy Much worse than last time
I am happy for the Penderecki recommendations. My old roommate had "Magnificat" and it was terrifying.
Butthole Surfers - "22 Going On 23" Super heavy sludge music with audio from a call-in radio show where a woman describes being sexually assaulted.
There's that Metallica cover of Breadfan where (I think its) Hatfield says "Mommy....where's Fluffy?" In a creepy voice at the end. I remember reading Metal Edge magazine around the time and someone else asked in the letters section, and the response was it was the punchline to a dirty joke. Wikipedia mentions it too but the story there is convoluted and said it actually belongs in front of "The Prince". I like the dirty joke story better. Regardless, always creeped me out way more than it should have. Also that version really rips!
Re:Butthole Surfers. That "Our Band Could Be Your Life" book mentions that the caller was supposedly a well-known lunatic in the area and would call that show regularly with wild stories. Let's be real, though, it's BS and a way to soften up the finished product. I adore the Surfers but that song is totally irredeemable and terrible from a decency perspective (granted this was their goal). There's no talking your way out of that one.
The Viacom logo "V of Doom" or "Wastepaper Basket of Doom", freaked out a lot of people in the 60s Looking like it was going to crash through the tv screen, haha, some of the YouTube comments are hilarious
Comus - Drip Drip , from the album First utterance Funnily enough i got the LP as a reissue from MOV today... The first track "Diana" is a good creepy folk tune as well, the whole album is creepy and off kilter but the acoustic instruments make it really listenable - for me anyway. Here s Diana - https://youtu.be/fhAmkEB94fA Don't enjoy it too much , originals are about a £1000 ...
This collaboration between Gene Ween and Guy Heller is also pretty disturbing and the kind of stuff OP may have had in mind.
Haha there's an entire subset of Genuinely Scary Songs right there - scary logos! The fanfare in the MGM/UA Home Video logo always gave me a little fright when I was a kid.. www.youtube.com/watch?v=s5eakWNPvyw
Scoring high on the creepy/disturbing meter, is the Tori Amos version of Eminem's '97 Bonnie and Clyde, where she speaks in a whisper as the murdered wife and mother, baby talk and all.
Alice Cooper - Ballad of Dwight Fry. One of the genuinely creepy and brilliant performances by Alice. The insanity is seething.
Again, not a "song", but the Lento movement from Schnittke's Symphony No. 8 is disturbing in it's cold, death haunted sound-world: