@ Happy Cheesecake, I never got the complaint about sailing taking too long. Especially once you got the whirlwind song that flew you from place to place.
And, I've played all the 3D Zelda games in the past two years, as until recently I had no game system that wasn't portable. Wind Waker overall improves upon everything in OoT, aside from the boss battles and the creepy parts of OoT. Majoras Mask wins in seriousness and scariness, while Wind Waker really has the best controls, dungeons, and story. TP is the most epic, with the best cinematics. However, it drags in the end, and the controls are a step back from Wind Waker. It also mostly gets rid of the instrument system, which was a shame.
My biggest complaint with Wind Waker is that it's so sparcelly populated, and that there are no decently large islands. Wink Waker takes the gold in visuals, because whether you like cell shading or not, Wind Waker is still an excellent looking game, whereas Twilight Princess was a bit outdated even when it came out.
If we do include 2D though, I say Links Awakening wins out in difficulty, map design, exploration, pacing, and music (mostly Tal Tal hieghts

).
Nah, I think OoT and Majora Mask wind out mostly with music, though TP had some really good songs, and the Wind Waker song on the open sea is great.
Best Dungeon I think goes to The Spirit temple. Not for it's difficulty or length, but it's design and that it really felt more or less like a temple.
So you know, the Wind Waker storyline is the one most likely to be explored in new games, unless they keep it with the handhelds. Maybe Spirit Tracks is this new "Hyrule".
Worst dungeon goes to Temple of the Ocean King in my book (is that it's name?). I hated having to retread though it over and over. I mean yeah, you didn't have to go through all of it every time, but the traps always reset, and I didn't want to do any of the puzzles more than once. Frankly I didn't like sneaking around to begin with. I would have appreciated being able to kill the phantoms much sooner.
Best moment in a dungeon was going back to the Forbidden Fortress with the master sword and getting to kiss the ass of every single damn Moblin There. That's what they got for those stealth sections earlier.
I'm not against stealth, I just like variety. Heck I love Beyond Good and Evil, which is full of stealth. In fact I liked the sneaking in The forbidden fortress quite a bit. I just really liked that I got to go back and kill all those moblins.
...yes, I've played every Nintendo made Zelda game (and Minish Cap).