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An addendum to the post about Small Yoshi: https://t.co/kLWbT8u7Iu Super Mario Run is also the only appearance of Small Daisy. However, until now, her model has never been extracted. I was approached by Twitter user @El_Libre_, who has generously offered to extract the data.
Version 3.0.4 of Super Mario Run, released 9 months after the game's launch, added Small Yoshi as Yoshi's form after taking damage, similar to Small Mario. This is to date the only appearance of Small Yoshi, as usually Baby Yoshi is used whenever a small form of Yoshi is needed.
In Paper Mario, the main hall of Tubba Blubba's Castle has an ornate ceiling (top) that can never be seen during gameplay, as all in-game scenes such as passing the upper corridor (bottom left) and the castle collapse (bottom right) have the in-game camera crop out the ceiling.
Super Mario Advance 4's data includes unused victory poses for all forms of Mario and Luigi, intended to be displayed after beating a level. In the finished game, Mario and Luigi simply quickly walk offscreen after completing a level without striking a pose.
Thanks to the new datamining efforts of https://t.co/aP3MSDXdpc user "Simpsons Dumper", the WarioWare/The Legend of Zelda: Majora's Mask crossover event graphics from Nintendo Badge Arcade, previously only seen as blurry screenshots, have finally been ripped in original quality.
In the data of Mario Party, unused early versions of characters' facial textures can be found. Here is a comparison between Yoshi's early eye texture (left) and the one used in the finished game (right).
Illustrations of Candy Kong in her Donkey Kong Country TV show design beating up various Kremlings and King K. Rool, from a set of Japanese Donkey Kong trading cards.
In the majority of 3D Mario games, Mario and Luigi's hat and hair are mutually exclusive, interchangeable parts of their models, never used together in the same scene. However, in Luigi's Mansion, there is a hair layer present underneath Luigi's hat in his main model.
The data for Pikmin on the GameCube includes an unused model of a Goomba head, called "kuribo.mod" (the Japanese name for "Goomba") internally. While the model appears normal from the front (left), turning it around reveals that it has a second face on its back (right).
In Super Mario Galaxy, whenever Mario touches dark matter, he dissolves into dust. However, a few frames before the dissolving animation begins, Mario's model loses its hands and most of its face. This can actually be seen in-game, although only from afar. Here it is zoomed in.