Despite having an overwhelming majority of friends who also think Windwaker is either so-so or outright horrible, it is by far my absolute favorite of the series-- second only to A Link to the Past (SNES). While others find the frequent sailing tedious, I love the opportunity to really relax in between active sessions of game play. Of course as Don points out, there is plenty to do for the gamers who prefer the "100% complete" style of playing videogames. The side quests are so numerous that half the fun is plotting a course that will carry you past as many of the islands you need to visit as possible on the way to your ultimate destination.
Not only that, but simply keeping a watchful eye for the pools of light that signify treasure will ensure that you are well occupied along the way. My girlfriend and I actually played through the first time with me at the controller and her at a laptop, keeping track of the various tasks and goals that had been mentioned in the game but that I wasn't yet capable of achieving. She had as much fun watching the story unfold and participating as a kind of "first mate" as I did playing.
All of this depth is on top of the great story line (which is a given for any Zelda game), and absolutely beautiful graphics. I personally feel the cell shading serves the Zelda universe well, unlike the more photo-realistic look that more recent games like Twilight Princess have tried to adopt. As an owner of the aforementioned game as well as the requisite Wii, I can tell you this newest version does not disappoint (nor does the system in fact), but it hasn't [yet] managed to claim the top spot in my mind despite the innovative input and superior hardware.
I could go on and on, but I've satisfied my urge to contribute to any conversation that includes Zelda, so I bid everyone a happy new year.