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It is hard to order the Zelda games because of strong nostalgic connections we all make with them. I have replayed OoT recently in the 3DS and that experience corroborated what I have been thinking for a long time.

I believe Wind Waker to be the best 3D Zelda. It have unsurpassed graphics, compelling story, and great exploration. Skyward Sword would be my second favorite. Combat is amazing -- fencing is not about special techniques but mastering simple movements and apply them with precision -- while the graphics and story are very good. The islands on the skies should have been richer and eventful. They way they presented was dull compared with the surface below. Ocarina of Time would me third choice, as the story is also good but not as compelling as the others. Some dungeons are not as elaborate as the other games and I don't like the fact Link can go to two time eras freely without any meaningful paradox. In almost a tie, I would place Twilight Princess, which seems to be an upgraded version of Ocarina of Time but also loose some points for not being original.

All that said, all Zelda games share great dungeon design, and at least good graphics and controls. I am not much a fan of Majora Mask. However, that is a game I tried once and never finished. Perhaps I should try it again.