Quite tough to choose. Bear in mind I haven't played all the games either (played everything but the GameBoy and DS ones).
Ancient Cistern from SS was pretty cool - nice visual style, and that boss fight was awesome (Koloktos, the big golden metal thing with 8 arms)
Spirit Temple from OoT had a great atmosphere - again, nice visual style, and the music works so well.
Forest Temple from OoT had a spookiness to it that I liked. Unfortunately, my crippling fear of Wallmasters meant I couldn't finish it for years :S Boss was a pain in the ass.
Earth Temple from WW - not much to say, I just liked it.
Quite liked
Ikana Castle from MM - music was just fantastic, and the boss looked kinda cool.
Goron Mines were good in TP, but the whole Iron Boots thing was annoying.
I liked
Snowpeak Ruins from TP because Yeto and Yeta were great

Loved the snowboarding bit and inadvertently helping Yeto make his soup while looking for the key

Music was good too; liked how it changed to be more warm and friendly when you entered Yeto's kitchen.