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 * The painting that acts as an entrance to Jolly Roger Bay (pictured) depicts a sunken ship. However, in Japanese copies of Super Mario 64 (except for the Shindou Edition), the painting is of a cloud of bubbles. In Super Mario 64 DS, the painting of bubbles is used regardless of the game region and the frame is light-blue instead of yellow.
 * The appearance of Mean Emcee, a boss from Wario World, parodies that of The Mask.
 * Bowser's Japanese name (クッパ, Kuppa) references the Korean dish gukbap; in Japan, the two have the same name.
 * In Paper Mario: The Thousand-Year Door, inside the Great Tree after the completion of the chapter, there is a room where a Jabbi is hidden in a bush. If shaken, the Jabbi appears and gives Mario a Mushroom.