Mine was the Ancient Cistern. I always loved water dungeons, so going through the first part of it, I already enjoyed it. When I figured I was getting near the end, I had basically just passed the half way point. That's when it turned into the underground, undead dungeon. So, it mixed some of my favorite things together. Water, darkness, death and decay! The whole dungeon was a nice size, and I just found it very enjoyable. Koloktos was great. I enjoyed the Sandship as well, but I didn't find it quite as creative as the Ancient Cistern (I love pirates though), so I enjoyed it especially for that reason.
All in all:
1. Ancient Cistern
2. Sandship
3. Sky Keep
4. Lanayru Mining Facility
5. Fire Sanctuary
6. Skyview Temple
7. Earth Temple
That said, I enjoyed them all very much. 3-7 might be interchangeable.