So a while ago I finished the Wii Zelda game I borrowed from Steve Minutillo, and yesterday I finished the Gamecube Zelda game I borrowed from Adam Parrish. I think Wind Waker (the Gamecube game) is my favorite Zelda game. This is partly because of its use of the Zelda myth.
The prevailing fanboy approach to the Zelda series is to try to put the games into some chronological order where there's an eternal recurrence of a hero archetype who keeps being reborn to fight the same evil over and over. In fact this is also the official approach, but it doesn't hold together very well. The details don't match up. Look at the intro story to Zelda 2: what should be a straightforward sequel is already a mess.
I prefer to think of every game in the series as being a different culture's telling of a myth--literally, the legend of Zelda--each emphasizing different things. Example: sometimes the hero visits a parallel universe, sometimes not, but in every telling with a parallel universe, the nature of the universe is different. It's like playing through all the video game adaptations of Journey to the West. On this view, trying to put the Zelda games in chronological order is like trying to unify the two creation myths in Genesis. It misses the point.
However, the Zelda myth is not that interesting on its own: it's the myth of The Kid Who Collected A Bunch Of Similar Things. Like if three-quarters of Lord of the Rings was Aragorn slumming it up and down Middle-Earth trying to find all the pieces of the Sword That Was Broken. I still need to play the N64 installments of the franchise, but Wind Waker had the best riffs on the myth of any Zelda game I've played.
First, the Polynesian-style setting was totally different, and it worked well. I think the ocean squares could have been reduced in size by about 25%, but it made the game world interesting the way loci of activity were scattered more or less uniformly across the map.
Also, in the other games I've played Link doesn't have much of a character arc. In Twilight Princess he starts out as a Luke Skywalker farm boy type who's thrust into greatness, but it doesn't really work because he's got the emotional range of your Kathy Ireland. He's a lot more expressive in Wind Waker with its cartoony graphics. He's also younger; his hero clothes are itchy and he's terrified, but he goes and is the hero anyway. It's typical Joseph Campbell stuff, but other games in the series don't even come up to that level. And it's especially effective with the Wind Waker backstory, in which the world is in the state it is because the last time someone ran through the eternal recurrence and told the myth, the hero didn't show up.
Bonuses: it's got a character who's effectively a coffinfish. I named my character "Zelda" in a tribute to the original NES Zelda game, which yielded yuk-worthy dialogue like "Hurry, Zelda! We must reach Zelda!". And while researching the much-loathéd character of Tingle, I discovered Freshly Picked Tingle's Rosy Rupeeland, the game that's a ruthless parody of the Zelda myth in addition to being a big "screw you" to fanboys everywhere.