This was a tough choice for me but I went with Bottom of the Well from Ocarina of Time. I just love the absurd amount of choice involved in this mini-dungeon. Most people probably just get the lens and get out, others get everything, and a few might just skip the whole mini-dungeon. You can do this mini-dungeon anytime after the Forest Temple, and reaching the mini-dungeon involves a time paradox and a cool song. Plus the creepy atmosphere is pretty much the scariest part of any Zelda game IMO.