Wind Waker is definitely one of my top 3 Zelda games. There's something so amazing to me about the colors and the expressions of Link and the fact that you actually have an adventure game with a bright, almost-happy setting as opposed to the standard doom-and-gloom of story-driven games. There's a sense of joy to be had when playing Wind Waker, because I feel they did a wonderful job of portraying the youthful heroism of Link, and the people who help him on his journey.
WW also has a sense of artistic direction, much like other cel-shaded games (Dark Cloud 2 immediately comes to mind for me as well). Whereas OoT immediately looks dated now, WW still holds its own because it represents an art style, as opposed to simply being the most graphically advanced thing possible at the time. Graphics get dated, style doesn't. Also, I may be the only person ever who actually enjoys sailing.
WW had my favorite Link, and my favorite Ganondorf by far. OoT actually introduced Ganondorf as a character as opposed to a faceless endboss, and WW successfully expanded on that character in my opinion. He's a little wiser, and more reflective, but he still harbors the same greed and hate that make him such a compelling villain. They've just been tempered by age, until he unleashes it in a vengeful but ultimately futile attack. The Triforce is beyond his grasp, but he still hates, and Link and Zelda's lives are a consolation prize. To me, Twilight Princess represented a huge step backwards in terms of Ganondorf, to the days of Ganon/Aghanim, where Ganon is nothing more than a puppeteer of a much more interesting villain (in this case, Zant) and simply makes a cameo appearance at the end.
I could continue singing the praises of WW forever, but I'll sum it up as such: I think Wind Waker (along with Majora's Mask), is one of the more ambitious and unique Zelda games, and I love it for the vision and risk-taking demonstrated. Fantastic gameplay is par for the course for a Zelda game; it's everything else that makes this one of my favorites.