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.

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

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

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.

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.

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.

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.

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.

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.

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.