Whenever I think of the Quake 64 soundtrack, Gloom Keep is always the first that comes to mind. The music has what sounds like moaning, chanting, and heavy footsteps that patrol the area. It's a good thing we don't know what it is.
The Necropolis was a track that always kept me on my toes as a child. It always made me fear looking around the corner incase there was an ogre waiting to annihilate me with its grenade launcher and which yeah there was one around the corner.
Termination Central plays in a futuristic base setting with technology everywhere, but even the music can give little ol' me a spook. The setting was different but the music was always frightening, but because it sounds like a robot patrolling around the base, looking for any intruders until it finally catches a glimpse of you and starts making a mad dash towards you. The noise of what sounds like machinery pumping as its footsteps getting louder and louder and it's about to catch you until it finally does.
Now for the last music I want to share, this one honestly gave me nightmares as a child. You're exploring a dark environment and you're hearing what sounds like moaning, but then you hear what sounds like a creature moving around, but where is it? Suddenly it starts making this shredded sound as it finally picked up your scent and is now on the move. It sounds getting closers as it could be in another room nearby, but then it sounds like it's behind you and it found you. You better run because it's getting closers and louder and then silence... Just when you thought it was gone only for it to make a loud shriek as it finally caught you. That scared me so much as a child, I always saw this creature as something slender like with long claws, spikes going down its chest, and this horrifying bird like face.