From the games I've completed:
1. Majora's Mask:
I LOVE this atmosphere in this game! And the 3 day cycle... it's just genius and I love the way it was incorporated into the game! Plus Stone Tower Temple is by far one of the best dungeons in the series.
2. Ocarina of Time:
A close second to Majora. I don't think I need to explain why it's this high up...
3. Skyward Sword:
I honestly thought this would be my favorite game but the dungeons weren't the strongest but were still great. I loved the character development in this game it can compete with Majora's Mask. I loved the motion controls and the new features included.
4. A Link Between Worlds
I've never played A Link to the Past but this game was still great on it's own and looked beautiful on the 3DS. The open world made it very unique and colorful. The amount of dungeons was insane (in a good way) but some were short. Plus, Thieves' Hideout is by far the worst dungeon I've played through. This was very unique and definitely a fav.
5. Twilight Princess
I loved this game on my first playthrough but the story is too similar to Ocarina. The graphics looked good at some points but was way to dark at a lot of points in the game. However, this game has the best dungeons in any Zelda game such as the City in the Sky, Arbiter's Grounds and the Temple of Time. Plus the Spinner...
6. Phantom Hourglass:
The touch controls made this game very unique and new on the DS. Again, the dungeons were short and very easy which was a miss. The sailing was ok I liked the customization involved with it. The Temple of the Ocean King made this great though! It was the best part of the game.
7. Oracle of Seasons:
I was surprised at this game. The dungeons, although short, provided a great challenge to get through and is by far the hardest zelda game I've played. The story makes this game not so good as it's pretty bland.
8. Spirit Tracks:
Although last on my list (for now), this game, again, added the unique train overworld and offered new challenges. However, it was too similar to Phantom Hourglass and also a lot shorter. The dungeons were an improvement over Phantom and offered more challenges involving the touch screen.