There are a large number of incomplete and test rooms in the code for The Wind Waker. Among them, there are even completely functional areas which were simply removed from the final game for various reasons. While not accessible via normal means, they can be accessed via cheat devices like Action Replay.

The Hylian text on Phantom Ganon's sword translates to 'Zubora Gabora.' Zubora and Gabora are the names of the two blacksmiths from Snowhead Mountain in Majora's Mask.

In game's maps and stages 3D model directory, there is a folder named "Tincle". The model presents the interior of a house, which only uses two textures. The first is a mess of paint with what appears to be a cat-eye face standing out. This texture covers the walls, ceiling, canvas, canvas borders, and much more. The second is a regular wood texture, soiled by black, green, red, blue, and yellow paint lines, which is used for the ceiling fan, table, and what appears to be a door. It is unknown what the purpose of this model was, nor why it was removed from the final game.

There's an item hidden in the game's code called the "Water Boots." They have no effect, but putting them on uses the same animation and sound as the Iron Boots. It's speculated that they may have been used for underwater swimming, or sinking underwater like the Iron Boots from Ocarina of Time.

Just as there was a "Dee Ess Island" in Phantom Hourglass, Hyrule Historia reveals that there was a plan for a GameCube Island in Wind Waker which never made it into the game. The only reference to it is a piece of concept art, shown in the book.

Behind Garlov's desk you can see the Bunny Mask, All Night Mask, Goron Mask, and the Keaton Mask, likely a reference to Majora's Mask. There also appears to be Chateau Romani on the shelf.

Inside the Master Sword chamber of Hyrule Castle, there are stained glass windows depicting the Seven Sages from Ocarina of Time, Link, Zelda and Ganon.

There is an Ocktorok sprite from the original Legend of Zelda on Manny's bag.

Real world constellations can be seen in the skies at night. These include The Big Dipper, Orion, and Cassiopeia.

Link yells "Come on!" when he calls Medli, Makar, or a statue using the Command Melody. This marked The Wind Waker as the first canon Zelda game in which Link speaks actual words.

The audio used for the ChuChus is an argument between two Japanese men, but sped up and played in reverse.

The man at the start says "At least I'm not balding" and the man near the end says "and looking like you are, people will think you're a monster".

Thank you to SteelBallJack for the translation. The audio has been updated from the source, as it wasn't reversed until now.

The game's main theme song is a combination of both the Earth God's Lyric and the Wind God's Aria, both of which are the last songs you learn in the game.

The portal sound is made with the same audio used for "the final hours" in Majora's Mask.

The Stars at night are not part of the skybox texture; they are actually polygonal vector models. This is done because vector graphics are infinitely scale-able and having a textured skybox would look pixelated if looked at through the telescope.

The game's file select screen undergoes a 7-minute day to night cycle, starting at whatever time the Gamecube's internal clock is set to.

The game's drastic change in art direction came from the desire to reinvigorate the Zelda development team. The hope was the new direction would inspire new gameplay ideas, which it did.

Several of the developers wives became interested in the game because of its visuals, despite not being gamers themselves. Eiji Aonuma's wife (from that point onward) began to play games he'd worked on.

Some of the music tracks in the game are either remixes or contain small renditions of music from previous Zelda games. The tracks are:

Windfall Island (Kakariko Village - A Link to the Past)
Dragon Roost Cavern (Dodongo's Cavern - Ocarina of Time)
The Portal Sound (Final Hours - Majora's Mask)
Inner Forest Haven (Kokiri Forest/Saria's Song - Ocarina of Time)
The Great Sea Theme (Overworld Theme - The Legend of Zelda)

The mountains around Ganon's Tower include a small cave that is usually not visible to the player. It is speculated that this may have been intended as a longer route to the tower instead of the straight entrance that Link takes in the final game.

The three goddess statues are actually a reference to Pikmin. The Din statue has a nose like a Red Pikmin, The Faore statue has ears like a Yellow Pikmin, and the Nayru statue has a crack that looks like a mouth, the defining trait of a Blue Pikmin.