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.

After development of the first game, Nintendo was considering developing a sequel with the working title 'Wind Waker 2'. According to producer Eiji Aonuma, the demand for a more Ocarina like game with Zelda made them reconsider the idea. Artist Satoru Takizawa stated The game would've been set on land rather than at sea.

"To tell you the truth, we had begun the initial steps towards creating Wind Waker 2 around that time. However, demand for a more Ocarina-like game was growing by the day. We did our very best with Wind Waker, and put everything we had into it…
However, Wind Waker 2 would have taken place in a more land-based setting, rather than on the sea, so that we could have Link gallop across the land on a horse.

But Link’s proportions in Wind Waker weren’t very well suited for riding on horseback, he was too short, and an adult version of Toon Link did not seem appropriate either. So, while we were stuck on those problems, we became aware of the greater demand for a more realistic, taller Link. High-budget live-action fantasy movies were also huge at the time, so with all things considered, we decided to have at it. I was on board with the project as art director, and started off by bringing [Yusuke] Nakano on to do the design for Link."

In the Italian release of the game, Tetra is named "Dazel", which is an anagram of "Zelda."

Since Link is left-handed in this iteration, he holds the Wind Waker in his left hand, while a conductor would more properly hold the baton in their right hand. Despite this he still uses the baton to adjust what time to play in, and his free hand to signal the pitch, just as a conductor would do, but with the opposite hands.

Link is voiced by Sachi Matsumoto, the same actor who voiced the Skull Kid from The Legend of Zelda: Majora's Mask.

In the E3 2002 trailer, the song "Riddles of Steel" from the 1982 film Conan the Barbarian is used. This song was also used in the commercial for Ocarina of Time, and was later used in the E3 2004 trailer for Twilight Princess.

Koboli, the postman found behind the counter found on Dragon Roost Island, was designed after the Postman from Majora's Mask. Through Zelda lore it is believed that the Running Man from Ocarina of Time is one of Koboli's ancestors, since the Zelda timeline makes it impossible for the Postman and Koboli to be related.

Link's body has animations for swimming and floating idly, but as all of the water in the game is opaque, the animations are never seen in the game. The only way to see them is by going into the game's unused test rooms, as they have clear water.

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.

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 idea to make The Wind Waker in HD came from the developers playing around with the Zelda HD Experience tech-demo. They used the same lighting from the demo on Link's The Wind Waker model, and his appearance had such a strong impact that they started to do the same with The Wind Waker's environments as well.

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.

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.

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 portal sound is made with the same audio used for "the final hours" 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.

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.