My top ten:
Forest Temple (OoT)
Stone Tower Temple
City in the Sky
Lanayru Mining Facility
Wind Temple
Hyrule Castle (TP)
Shadow Temple
Great Bay Temple
Snowpeak Ruins
Ice Ruins
(I'm in the process of reviving a bit of discussion from the old World of Zelda stickies, so it might seem familiar, but feel free to post and share your views.)
The Zelda series is famous for its puzzle and challenged filled dungeons, each offering something different in variety which has...