Madame Fanadi, the fortune teller says strange words while looking into the future. When you reverse her gibberish, you get coherent sentences. If you ask about love she says, "Wait... loading takes awhile." If you ask her about your career she says, "What am I talking about?"

There are some The Wind Waker leftovers in the game. These are the Wind Waker item itself, Bomb Flowers and some other items. The file 'itemmdl.arc' contains models of 21 items from The Legend of Zelda: The Wind Waker which suggests Twilight Princess uses The Wind Waker's engine.

On your way to the Forest Temple, you come across an armored skeletal warrior known as the Hero's Shade. He was a famed swordsman in Hyrule, but died with eternal regret of never having passed on his knowledge in the art of the sword. According to the Hyrule Historia, the Hero's Shade is the spiritual manifestation of the Hero of Time, the Link from Ocarina of Time and Majora's Mask.

Originally, the magic meter was planned to be in the game, and can even be seen on one of the screenshots on the back of the box. Unused text left in the game reveals Link would need magic to transform into his wolf form.

Twilight Princess is one of the few Zelda games that does not have a magic meter. As such, there is no need for Green Chu Jelly, which is an item used to refill magic in other Zelda games. However, in the Wii version, it is possible to obtain Green Chu Jelly through normal means. But it is only possible once, in the "Cave of Ordeals", room 19. Carefully kill all of the purple Chus and let a Blue Chu and and Yellow Chu merge. Kill it and then scoop up the remains with a bottle. Link will now be holding a bottle of Green Chu Jelly. It has no text, description or effect whatsoever. However, performing this trick in the GameCube version produces a Purple Chu instead.

In the E3 2004 trailer, Nintendo reused voice clips of Nobuyuki Hiyama (Ocarina of Time's Link) instead of Akira Sasanuma, who provided Link's voice in the final version of Twilight Princess.

The fisherman from Ocarina of Time can be seen in a photo at Hena's fishing hole. Hena thinks she is related but she "can't exactly PROVE it." She also scratches like the fisherman, further linking them together.

In Twilight Princess's prerelease, the Twilight world was black and white. This artistic choice was not carried over to the final version.

Twilight Princess was originally going to be a sequel to The Wind Waker. A presentation by director Eiji Aonuma contained a reference to the working title The Wind Waker 2 and it was said to use a similar graphical style. Nintendo of America told Aonuma that North American sales of The Wind Waker were sluggish because the cartoon appearance created the impression that the game was designed for a young audience. Concerned that the sequel would have the same problem, Aonuma expressed to Shigeru Miyamoto that he wanted to create a realistic Zelda game that would appeal to the North American market.

If you reset the game while your hand is just above the quicksand in arbiter's ground, you will be put in to a glitchy version of the game without icons on the screen.

If you complete the STAR mini-game in Hyrule Castle town, go outside (while in human form) and approach the three ladies standing by the door: Kili, Hanna, and Misha. When talking to them they'll squeal with delight and provide you with three hearts before running away. It is assumed that these women are Link's fan girls, as they say "EEEEEEK! It's HIM!".

The track used for The Legend of Zelda: Ocarina of Time commercials is "Riddle of Steel" from the 1982 film Conan the Barbarian. This same song was also later used for The Legend of Zelda: Twilight Princess E3 2004 trailer.

Midna doesn't have a reflection. In Link's house there is a mirror that fails to show Midna's reflection when she's on top of Wolf Link. Midna's reflection also doesn't appear on ice.

The Master Sword being a sword that would get pulled out from its pedestal by those chosen appears to be derived from the Arthurian Legend of Excalibur, also known as the "sword in the stone". Similar to how King Arthur was divinely chosen to be able to pull out Excalibur, Link was given the power by the Goddesses to pull out the Master Sword. Because of these similarities, the Master Sword was renamed to "Excalibur" in the French localizations of The Legend of Zelda: A Link to the Past, The Legend of Zelda: The Wind Waker, and The Legend of Zelda: Twilight Princess.