Windwaker is the best Zelda game when it came to exploration and discovery. Not in the traditional sense, where you find loot and get better shit. But in the sense that you see something in the distance and have no idea what it is.
Besides Windwaker and Twilight Princess, every other 3D Zelda game seems puny and lacks the excitement of exploring the world. I think a lot of people forgot how big Twilight Princess is.
It turns out scale is what makes 3D Zelda games great to me.
No, that's Majora's Mask. Seeing a fairy tower and not knowing what it is, "where's Epona?", finding the ranch;etc. Majora's Mask is pretty much tops when it comes to exploration because everything adds something to the game and has a purpose.
In Wind Waker, it's usually nothing of worth and a couple hundred rupees at best.
I loved exploring Wind Waker because I was just OCD like that and I had about every tile on that map filled out by the time the triforce hunt occurred. Not sure I'd get the same enjoyment out of it now, though.