Hyrule Castle has three unused stain glass windows of three characters from the The Legend of Zelda: The Wind Waker:
•The Deku Tree
•The Deku Tree
The European release's music in the Sword Dojo is a bit different from the Japanese and US releases. The reason for this change is unknown.
Vaati's laugh is just a shortened version of the Happy Mask Salesman's laugh from Majora's Mask.
In a cave digging in Castor Wilds, the Japanese word "ã‚‚ãã‚‰" ("Mole") is hidden out of the game's visible area.
In the PAL version, the description for figurine #108, Ice Wizzrobe, suggests hitting Ice Wizzrobes with the Fire Rod, an item not available in the final version of the game. This was corrected in the USA release.
There's an unused animation for the decorative mailbox that appears above the post office in Hyrule Castle Town. The level of animation suggests that there were to be fully functional mailboxes in the game, much like with The Wind Waker.
Malon, who sells Lon Lon milk in Hyrule Town, can be heard singing Epona's Song from Ocarina of Time when you are near her.
In the opening cutscene of the game, the story tells that a "tiny Picori appeared from the sky, bringing the hero of men a sword and a golden light". According the the official Legend of Zelda timeline, The Minish Cap is the second game chronologically, taking place only after the events of Skyward Sword. This might suggest that the Picori is the incarnation of Link from Skyward Sword, bringing the master sword down from Skyloft. In addition, the man brandishing the sword in the mural that is depicted as the text displays appears to be some incarnation of Link.
Bob-ombs from the Mario series make a cameo as dungeon enemies.
The Ocarina of Wind's tune is the same as the Warp Whistle from Super Mario Bros. 3 and the Recorder from the original The Legend of Zelda.
In the code of the ROM is what appears to be a man wearing a pair of underpants, a cape, and a crown. It's very out of style and obviously just a scribble, but it also includes a full walking sprite-set, as well a number of other random animations.
In the first dungeon, you come across a red-capped mushroom enemy that walks around spraying spores. The enemy is named "Puffstool", and is actually a reference to an enemy found in Pikmin also named "Puffstool" who sprays spores to infect Pikmin and turn them against you.
There are a number of unused audio clips still present within The Minish Cap. Many of these unused pieces are renditions of songs and sound effects from previous games (e.g. the Lost Woods from Ocarina of Time, attached).