I grew up with FireRed, and I'm pretty sure they've edited the FireRed music from the original Red music, due to its overall creepiness. But, I did find (supposedly) original samples of the Japanese Pokemon Red game music, and it was somewhat chilling. However, it's mostly Lavender Town's background that makes the music scary. The whole dead mother Marowak, the possessed Challeners, the only place known for laying Pokemon to rest makes it especially scary.
However, when I was playing through Pearl for the first time, I went into the Old Cherau and it was what I could truly call scary. The picture that would stare at you when you had your back to it, but would stop when you looked, the whole little girl ghost thing, and the truly scary music made the Old Cheatau win this one.