Maybe I'm in the minority here, but I think The Wind Waker's overworld is by far the best. No matter how many times I play that game, I'm still caught off guard every once in awhile by something new. It's really quite a magical experience to sail the vast, open sea and run aground on hidden islands. And the nice thing is, while the game's linear, your exploration doesn't feel that limited.
Second is Ocarina of Time. Much of it is empty, but (since you know TWW's is my favorite, I can say this) emptiness in itself isn't bad. Once again, exploration is rewarded; snag Epona early in the game and you can wander Gerudo Fortress before completing the Forest Temple. It's this level of freedom that gives Ocarina its charm; and in every area you enter, you always feel there's something new to discover.You're not limited or held back. Third, Majora's Mask has an incredible overworld that may be objectively better than Ocarina's: it's more tightly-packed, there's more to do, and it's kind of hard to be bored while exploring it. The problem is that I like some semblance of realism and randomness in my map layouts and MM sacrifices that for utility. It's still a great overworld.
Then we come to Twilight Princess.
The field itself is quite nice. There are a lot of good ideas in its construction; having separate sections gave the developers some freedom to offer new gameplay challenges and whatnot. Unfortunately, much of the field is a lost opportunity. Forget about being empty for a moment; there's very little to do. This is actually a problem shared by The Minish Cap; confined as you are to narrow passages and isolated villages at any one point in the game, you may explore for a half hour, only to find you've done everything there is to do. There may be a statue here or there you can move later on, but in large part, traversing the field looking for that is just going to end up being a nuisance. This stands in stark contrast to, for example, The Wind Waker, where every new island you sailed to might offer at least some reward, and there were 49 islands, treasure chests galore, etc. And that's another thing: with money being so easy to come by and so useless in TP (unless you're willing to do the agonizing quest for a bigger wallet), a few rupees is hardly a reward. Yet that's exactly what we're usually given.
Still, the field's not bad in itself, it's just utilized poorly due in part to the game's structure, the meager rewards, and the uninteresting environments. The rest of the overworld (towns, mountains, forests, etc.) is where the real problems start to set in. TP has a Wild West theme. It's really strange and out of place. What we're left with is villages like Kakariko which do little to stir the imagination. Compare Kakariko in Ocarina of Time, or Clock Town in MM, or Windfall Island in TWW, to Kakariko in TP. Where the former were filled with vibrant, rich characters, tons of nooks and crannies, and visual designs which encouraged exploration, the latter was filled with dust, sarcastic, uninteresting characters, and few quests of much merit after the beginning of the game.
Towns in TP were small, had little to do, and barely served a function after they had their one spot in the story. You could run down the list and TP would pale in comparison to its 3D counterparts. And while there were some genuinely nice areas (Zora's Fountain and the forest in Ordon), other potentially nice areas (The Lost Woods) were ruined with confined approaches that in many ways inhibited genuine exploration. This is a problem partly shared by Majora's Mask, but MM had a fix; beat a dungeon and the area opened up. TP didn't offer anything like that. Unfortunately, its world, lacking a sense of history, proper direction (art or otherwise), interesting towns, or an engaging atmosphere, was dead in the water.
There's another fair comparison to make, by the way. Okami was released around the same time, and its overworld rivals (probably beats) all the 3D overworlds of Zelda games. While it does limit what you can do at any point in time, the limits are hardly worth complaining about, because it still offers so much. It balances openness with utility, looks natural, and offers a decent amount of enemy encounters without limiting freedom. Amazingly, every town is nearly as vibrant, populated, and worth exploring as Windfall Island (my favorite town in any Zelda game). Had TP offered an overworld remotely like this, it may also have rivaled the other 3D Zelda games in scope. If it opted for emptiness instead, it could at least have evoked the atmosphere of Shadow of the Colossus. What we got was a dusty, empty, nearly unpopulated, canyon-ridden overworld. None of these elements would necessarily be bad on their own, but coupled with the gameplay decisions made in Twilight Princess, they sort of destroyed the whole experience.
That is why it's my least favorite overworld of all the Zelda games, even if there are some areas that are promising.