You pose a tough question, but make a good case with the Snowpeak Ruins. It also ranks highly in my list.
Let me think out loud here, it's not one of those things I can just say on the spot. I have to say overal, I like the offerings in Ocarina of Time and Twilight Princess best, with Skyward Sword not far behind. Majora's Mask is weaker on the dungeon front, albeit with one massive exception, and Wind Waker easily loses out, with none of them getting anywhere near the series' top. I'd say the Tower of the Gods is by far the best in that game, but it's way too short and it's boss isn't exactly an original concept.
Let's see;
Forest Temple OoT: I like the abandoned haunted mansion style, it has a good theme, looks great, cool puzzles and an amazing boss.
Water Temple OoT: Dark Link. Should be enough to mention, but it's also great how the entire thing revolves a single feature.
Spirit Temple OoT: Probably the best front facade of any dungeon, it's also nice and big, the time mechanic is great and the boss equally so.
Stone Tower Temple MM: The use of the Light Arrows to flip the dungeon is brilliant, brings awesome new mechanics and totally blew my mind when I first saw that. Terrible boss though.
Arbiter's Grounds TP: Great overal, great use of items and very original, creative puzzles. Best boss in the history of bosses, with equally great boss music. Why is there no Boss Rush mode in TP?!
Snowpeak Ruins TP: Very similar reasons as the Forest Temple from OoT, looks great, great theme with fun characters and a cool boss. No pun intended.
Temple of Time TP: Gorgeous visual design, great mini-boss and brilliant puzzles which have to be done twice in different ways, once on the way up, once on the way down.
City in the Sky TP: TP's awesome streak ends with this, which is great because it features the greatest item ever in a big way. Lousy boss though sadly.
Ancient Cistern SS: Looks great, cool mesh of two themes with a good final boss. The best part though is the part where you climb the rope.
Sandship SS: Like the Forest Temple OoT and the Snowpeak Ruins TP, I like these dungeons inside "real" locations, also probably the best build-up to any boss.
Skykeep SS: Probably the best 'final dungeon' yet, I loved the idea that the entire dungeon was one big puzzle, with rooms that could switch places.
I think those are my favorites, but this didn't make it much easier... Absolute top, I guess, would probably be the Forest Temple, Stone Tower Temple and the Arbiter's Grounds. I think I'll pick the Forest Temple as absolute winner, due to the fact it ticks all the boxes and is good in it's simplicity, and it's polished ideas. Less is more, as a certain architect once said. I also can't think of a single thing that is even slightly disappointing about it.
So, Forest Temple from Ocarina of Time.
