Big Brain Academy
June 30, 2005
In the "Get In Shape" mini-game, one of the picture formed by the shapes represents a Piranha Plant coming out of a pipe.
In the "Missing Link" mini-game, one of the images is Mario's symbol (a circle with the letter "M" in the middle).
Big Brain Academy: Wii Degree
April 26, 2007
In the "Speed Sorting" mini-game, an image of Racoon Mario from Super Mario Bros. 3 is featured as the right answer to "Has a tail!" and one of the wrong answers to "Plant matter!"
Super Mario Maker
September 10, 2015
One of the unlockable costumes that Mario can wear in the game by using a Mystery Mushroom is based on Dr. Lobe, and when worn it replaces some of the sound effects with sounds from Big Brain Academy. He pulls out a star as a taunt
Copyrights for both series are held by Nintendo.