Christmas Rushed: According to Aonuma, the game was set to release on a strict date and couldn't be delayed any, this resulted in two possible dungeons (Inside Jabun and a third Sage temple) being cut, and the infamous Triforce quest being put in as padding. The response of Shigeru Miyamoto to this trope is the current page quote.
Fado is an in-series example. He shares his name with a female Kokiri from The Legend of Zelda: Ocarina of Time. Notably, Ocarina of Time was originally going to have a Wind Temple, and that Fado was likely intended to have been the Sage of Wind, so him having the same name is likely a reference to that.
Gohma. Not to be confused with the first boss of Ocarina, which was an arachnid, not a myriapod.
Two more dungeons note Inside Jabun and a third Sage temple were planned to be in the game, but eventually had to be cut due to the game being Christmas Rushed. They were thinking about having them be added in the HD Remake, but decided to stay true to the original version of the game, and instead just made the infamous Triforce collection quest far less tedious.
In the original E3 trailer, Link wore clothes in the style of Link from the original game instead of Ocarina Of Time style clothes.
Concept art shows various unused Tetra designs, including an Ambiguously Brown Zelda.
Certain beta screenshots show a Link with blue eyes instead of black eyes like in the final product.
"Water Boots" are an unused item in the games data.
The first trailer shows that Link originally had a sneak ability for the fortress section of the game. It was later replaced with using barrels.
When you enter Gohma's boss room in Dragon Roost Cavern, if you do not move for a while, the King of Red Lions will tell you "A mighty enemy stands before you!" and give you advice on how to fight Gohma, even if Gohma hasn't appeared yet. Similarly, if you don't attack Phantom Ganon the proper way on your first encounter, the Pirate's Charm will activate and the King of Red Lions assures you that you can strike back his projectiles with the Master Sword's power to repel evil.
Nintendo consulted a retired Toei animator who worked on Toei films of the 1960s for direction on The Wind Waker's art style, explaining why the game's cel-shading style is so different and more polished than other games' cel-shading.
As per Zelda tradition, when you defeat a dungeon boss, you have a moment to relax and get the heart piece before going to the teleport to exit the dungeon. Typically, ambient sounds or a calm relaxing melody plays. In this game, for the first two dungeons, the first few notes of the "final hours" music from Majora´s Mask play, only slowed down. This only happens in the first two dungeons and it´s hard to notice considering most players will just get the heart piece and get out of the dungeon, but it´s there. Only Nintendo can make a remix of a creepy theme so peaceful.