IMO it's the best 3D Zelda after Ocarina of Time. It's no-nonsense, nice and dark, vast, has a real sense of adventure. I doubt we'll get one any time soon but I'm holding out for a HD remake.
*disclaimer= I haven't played Majora's Mask yet!
I don't like Skyward Sword at all, and I never played Twilight Princess. But I doubt it can beat Majora's Mask!
Majora's Mask is an amazing game, behind OoT only because of its comparably (not absolutely) dull/repetitive storyline, slightly less exciting world, and dull/repetitive soundtrack. But it almost makes up for it with its improved temples, way more challenging enemies, and cool time mechanics. And it's ahead of its time in terms of graphics and overall detail. It's also by far the hardest Zelda game I've ever played, definitely aimed towards serious fans who have played OoT and want something a level higher. Windwaker, in contrast, seems to be for new players and is actually missing a lot of gameplay mechanics from MM. It's easier than OoT. Still a great game for other reasons.