Hm, let´s see:
*Password music in CVII and Nightmare in CVIII when I was a child... That tracks are simply amazing, and for me they gave the perfect ambience to a CV game. When I hear it the first time in case of CVII, I write so fast the password, so I do not hear the track. The same case with Nightmare: I want to finish the stage ASAP.
*Legion fight in SoTN. Hearing the corpses/people screams was really spooky and awesome at the same time.
*Fighting a topless Medusa in SCIV... ´nuff said. (With all the policies in video games at that time).
*I can´t remember at this time where exactly is, but there is a pre-boss room in CVRoB that have a skeleton, that if you hit it, its goes to the wall and disapear... with not explanation to me. Add the music, and we have another unsettling moment.
*The fight with the Forgotten One from LoI. Beggining with the creepy sounds from the background before entering his room, and the whole fight against him/it.
*The whole Succubus part in SoTN. Hear the background music while fighting her is really awesome!!!
*In SoTN again, the music in the Abandoned Mine remind me alot (I dunno why) to music from a horror movie.
*The room before fighting Dracula and Death in PoR, with the image of the Dragon, the woman and the child... speechless...