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In Super Mario Maker, all of Costume Mario's forms in the Super Mario Bros. style have a special pose activated by pressing Up, called "appeal" internally. There is an unused "appeal" sprite in the code for Weird Mario as well, which makes a third button appear on his overalls.
Artwork from the cover of the manual for Super Irmãos (Portuguese for "Super Brothers"), an unlicensed distribution of Super Mario Bros. from Brazil.
The Midas River minigame in Super Mario RPG contains a river background that scrolls diagonally. In the game's data, it is saved as a square image with several rivers that uses screen wrapping to appear as one uninterrupted river (explanation in image).
This group artwork for Super Mario Bros. 3 is notable in that every single character in it with a visible eye color (eyes that are not simple dot pupils) has blue eyes. Bowser's eye color was changed to red since, so this would no longer be true if the image was recreated today.
@GamerZardEX While this cannot be seen in-game without modifying the camera code, there is something similar in Mario Party 6, where Goombas are loaded separately from their eyebrows when off-camera; see attached image.
In Level 3 of the "Opening Night" microgame in WarioWare: Smooth Moves, Samus Aran from the Metroid series appears playing a cello (left). This is likely a reference to the NES version of Tetris, where upon reaching a high enough score, Samus also appears playing a cello (right).
Official artwork of Bowser laughing at a screen depicting logos of Internet video streaming services from a Japanese Wii U informational brochure. Although it may appear that the TV screen has been edited in from different artwork, this is the only existing version of this image.
Both Paper Mario: The Thousand-Year Door and Super Paper Mario contain remnants of a design concept for Princess Peach with shorter hair; seen on Peach's chapter intro medallion in the former and found as an unused quick edit of the sprite in the data of the latter.
In Super Mario Bros. 3, only one out of eight levels in Grass Land (1-2, top middle) has ground that resembles grass due to its color, while the others contain no grass. In addition, the Grass Land map has yellow ground. Worlds 3, 4 and 7 all contain more grass than Grass Land.
The animated stickers featured on Nintendo's official LINE account are drawn to have every frame resemble official 2D Mario artwork as closely as possible. Here are the very few singular frames where characters are drawn in a nonstandard manner.