1. Sandship
2. Sky Keep
3. Skyview Temple
4. Fire Sanctuary
5. Earth Temple
6. Ancient Cistern
7. Lanayru Mining Facility
What's weird is that there was another thread on this a month ago, and after playing through hero mode my list changed almost entirely- before it was 1. Sandship, 2. Ancient Cistern, 3. Sky Keep, 4. Lanayru Mining Facility, 5. Fire Sanctuary, 6. Earth Temple, 7. Skyview Temple
My original reaction was that the game built up slowly to a peak at the Sandship then took a dip at the Fire Sanctuary and finished strong at Sky Keep. My opinion now is that the game started off strong with the first two dungeons, went down a little in the third and fourth, shot back up at the Sandship and finished strong with the final two dungeons. The uses of the timeshift stones in the Lanayru Mining Facility seemed less impressive after using it to change a whole environment at once in the Sandship IMO.