I was a big fan of the Snow Peak ruins race in TP. It was totally different than any of the other "races" in the Zelda games. There were multiple ways to go, and it was challenging. It's got my vote.
I would make a Skull Kid mask that you could use to never get lost in the lost woods.
I would also make a four swords mask, for Majoras Mask multiplayer action.
I honestly don't care much to play the handheld ones. Links Awakening was good, and I did beat the Minish Cap. But Phantom Hourglass was a giant pile of suckage, and I imagine Spirit tracks is just as bad. Never played the Oracle games... I just find it too difficult to get into the hand held...
Mine only froze on me once (so far)... I had just gone through the Woodfall temple, and did the butler race, when it froze up right at the end. I had to do all of that over again.
Looks like the majority wins here. Ancient Cistern for me as well. I especially loved the "dark" section at in the basement of it. Never saw that coming in a "water" temple.
ChuggaaConroy and NintendoCapriSun both have pretty good LP's of the WindWaker. Actually AngryPoncho is doing one now that's only 7 or 8 episodes in, and it's pretty good too so far.
Of course... their LP's are more playthroughs than walkthroughs. It would be nice if ZD could get more...
A cave of ordeals type dungeon in the graveyard would have been great. But I too, noticed that there literally was no point to the graveyard other than getting to Batreaux's house. At least they put a light tear there that you needed to collect in that last trial.