I think the creepiest song in the Zelda Series is probably when you Encounter Zant in TP at the Twilight Realm. It creeped me out, the weird bell sounds and everything else. *shivers* Jeez...freaky.
Zant's Theme wasnt the freakiest thing i've ever heard, but it's up there.
Second to that is the Stone Tower temple music from Ocarina of time. The unnatural sounds that echoed throughout the track ran chills up my spine.
The music that plays in all of the Light World dungeons of aLttP, or the music in the Earth Temple in WW. Mostly because I was still young when I first played these games and heard the music. I still think the music is rather creepy though.