I love both of those as well! 

There are so many good ones to pick from. I can someone imagine Zelda U doing absolutely everything right with fantastic new mechanics and designs and have piss poor dungeons just to make us all sad

Was going to say ocarinas shadow dungeon but snowpeak ruins was superbly done. Still,as a fan of darker zeldas, the shadow temple just teases me as to what the series can do.

I'm, not going to lie, I am surprised that I am the first that is going to say this - Dodongo's Cavern from OoT was definitely my favorite. It's where my name stemmed from, and I don't just love the dungeon, I love the sequence of events leading up to the dungeon. Goron City and the little puzzles you have to figure out in there in order to get to the dungeon is just great. Snowpeak Ruins is right up there for me as well though : )

Even though I like those, I really think all 3D Zelda dungeons are pretty bad compared to the ones in Zelda's 1, 2, and 3. I don't like the presence of puzzles at all. I have hope that there won't be any in the new Zelda, as Aonuma has been alluding to it. I really think that the way Dark Souls handles dungeons is the way Zelda should. Dungeons used to be scary with the overworld serving as a sanctuary from them. Zelda lost that feeling, so I hope that returns.

I have only played one 3D Zelda game and that's Ocarina. My favorite temple is The Water Temple.

I know it's your opinion and I respect that, but personally if the new Zelda has no puzzles I'll be done with the series. It's what defines Zelda to me, and to have that taken away would make me really sad =P

I love Snowpeak because of how organic it feels. But my all-time favorite is the Ancient Cistern.

Sand Ship, a lot of the dungeons in SS are well designed but the concept in the Sand Ship is imo the best in the series.

Seems like we're getting to that point where we love Skyward Sword and are ready to hate the next game in the series ^_^.

Sandship is my favorite. I also really like Dodongo's Cavern and the Temple of Time in Twilight Princess. And the Sky Temple, cause the dual clawshots made me feel like Spider-man.

Good choice. Although, I prefer the original version boss battle.

As for my choice, it's pretty difficult to me as I have a lot of favorites:

Ganon's Castle (Ocarina of Time)

Spirit Temple (Ocarina of Time)

Water Temple (Ocarina of Time)

Ganon's Tower (A Link to the Past)