Thought this would be a neat poll that might blossom into a beautiful off-topic conversation about something in OoT.
I like the Nocturne of Shadow most. Its notes are easy on the ears and it runs smoothly. It's also easier to play the full song on the Ocarina alone than the others (I can't be the only one who has attempted that). And I like pretty much everything about the Shadow Temple, and more than that, the Well of Three Features. Probably because Zelda dungeons all tend to feel like they were built just to be dungeons, house bosses, and be hard to get through. The Well and the Shadow Temple feel like they once had unspoken purposes.