I'd go with
1. Ocarina of Time - The Forest and Water Temples in particular are extremely replayable for me. They are nonlinear and can be completed in different ways/orders. I've obsessed over the Water Temple in the past by trying to figure out the fastest way through it. At one point I had a save file just for the Water Temple, and I've probably beaten it several hundred times. The child dungeons weren't my favorite, but I loved the adult dungeons except for the Fire Temple. I thought the design of the Spirit Temple was pretty clever as well.
2. Skyward Sword - I love the Sandship and Sky Keep. The Sandship was another dungeon that I created a save file just to replay and analyzed like crazy to figure out the fastest way through. I didn't like the Earth Temple or Fire Sanctuary, but I liked the aesthetics of the Ancient Cistern and the time shift mechanic introduced in Lanayru Mining Facility.
3. Twilight Princess - I only loved the Snowpeak Ruins, but I felt that the game had consistently high caliber dungeons. If I had to criticize one, it would be the Palace of Twilight, but other than that I wouldn't have anything bad to say about any of them. Snowpeak was my favorite for several reasons - the atmosphere, the ice block puzzles, the misleading directions, and as far as I know the only instance in the series where knowledge of the location of a key can speed you through subsequent playthoughs (the key buried in snow). I also particularly liked the aesthetic of the Lakebed Temple. Even reaching the temple seemed awesome because it's hidden in a lake, and I thought the flowing water led to some good puzzles.
4. Majora's Mask - Overall it just didn't have many dungeons, but I loved Snowhead, Great Bay, and Stone Tower Temple. Woodfall is kind of boring compared to the others.
5. Wind Waker - The dungeons were good but not great. This is the only game that didn't have a dungeon that really stood out that I loved. The Tower of the Gods and Earth Temple were probably my favorites. I liked the use of Medli for puzzles a lot, and transporting statues also led to good puzzles.
One pattern that I noticed is that the two games with the best out of dungeon experiences ended up at the bottom of my list. Ocarina of Time and Twilight Princess had most of their best moments within dungeons. To me it seems clear that the game designers spent a greater portion of their time on dungeons for these games and it shows. Skyward Sword is kind of in between.