I would say most of the dungeon music in OoT was pretty creepy. I'll give my opinions on some of them.
--The Deku Tree--
This music gives me a sence of loneliness. It seems to echo throughout the Deku Tree, making it feel empty and dead. It also inspires a sence of exlporation in me, like exploring an ancient, primitive, tomb.
--Dodongo's Cavern--
This music is pretty quiet, it sounds like it should - like a cave with creatures crawling around inside. I hear a weird screech ocasionally throughout the song, it makes me think there are more than a few things lurking around inside.
--Jabu Jabu's Belly--
Very eerie music, it seems that you can hear the whale groaning while you are inside. Like all good zelda music should, it matches the envoirnment well. It is a pretty creepy song, it never fails to make me just a little weirded out that you are inside a whale.
--Forest Temple--
I think this theme in particular stands out as one of the most eerie songs, if not the most eerie song in the game. This music seems to give the dungeon life, it seems as though the dungeon is alive, watching you. It also has an earthy sound, and much like the Deku Tree theme, manges to make you feel very alone. I know this sounds contradictory, but that is the impression I got.
--Fire Temple--
At the begining of this track you can hear the wind blowing. This made me think the dungeon was desolate and lonely. Along with the strange chanting, this makes for a mildly creepy song.
--Water Temple--
This track was strange, yet soothing, it seems like you can hear everything echoing in the water. It makes me think 'cavern' as much as Dodongo's Cavern theme did. It's eerie, but in a subtle way.
--Shadow Temple--
Suprisingly, I don't consider this the creepiest music, rather it seems more along the lines of disturbing than creepy. The strange wail that repeats throught the song, this is the only dungeon music track that didn't make me feel alone. I felt like there were long dead beings watching my progress, pleading for help that has come to late for them.
--Spirit Temple--
I didn't find this very strange at all. While it did inspire a sence of lonliness, it just wasn't creepy to me. It seems like you are treading on holy ground for the Gerudo people, a place which is of great importance to them. I wouldn't call this track very creepy, it does make me feel alone though.
All in all, the top three creepiest tracks in my opinion were the Forest Temple theme, the Water Temple theme, and the Deku Tree theme. With runners-up being the Shadow Temple and Jabu Jabu's Belly themes.
I would say that most of the dungeon music in OoT was creepy and strange, and after listening to them again I also feel that they were going for a sence of lonliness in the dungeons as well. I don't think that goes for the rest of the game as much though, I think they were trying to go with eerie and lonely just for the dungeons and mini-dungeons.