Rosalina's Storybook was written by Yoshiaki Koizumi, who wrote it at night without anybody knowing what he was doing. The following day he presented the story to Shigeru Miyamoto, who was surprised when Yoshiaki told him that nobody else knew about it.

Strangely, when the player plays as Luigi in the mission "Luigi and the Haunted Mansion" the trapped Luigi will still call out for Mario. This could either be something the developers missed or the fact that he could have been expecting Mario to rescue him.

Star Bits from Super Mario Galaxy and Gratitude Crystals from The Legend of Zelda: Skyward Sword are based on candy. The candy is called Konpeitō and is popular in Japan.

There is a hidden toy train in the Toy Time Galaxy. It serves no purpose and was likely a gag by developers.

On the game's cover, certain letters in the title have a small star under them. Reading only these letters spells out "U R MR GAY" - either a funny coincidence or a joke played by the cover artist. The letters sparkle on the title screen as well, leading more credence to the joke.

Unused models for Bully, an enemy from Super Mario 64, are present in the game's data, complete with animation.

In the Deep Dark Galaxy, on the shrinking planet , you can crawl into the blue house and see the inside of the of the planet. Also the walls are not solid on the inside, so you can walk out.

The Japanese versions of Super Mario Sunshine and Super Mario Galaxy have different Engrish win messages when collecting a Shine/Star. In the Japanese release of Sunshine, the phrase "Shine Get!" is shown every time Mario obtains a Shine, which was changed to simply say "Shine!" for the English release. In the Japanese release of Galaxy, "Star get!" is used when the player acquires a Star, and "Grand Star get!" is used when they get a Grand Star. In the English release, the grammar was cleaned up to read "You got a Star!" and "You got a Grand Star!", but the Korean release of Galaxy reverted this back to "Star get!" and "Grand Star get!"

The battle against Megaleg is based on a scrapped concept of the final battle in The Legend of Zelda: Ocarina of Time, where Link would have to scale Ganon's (then-colossal) body in order to defeat him.

A tech demo developed by Shigeru Miyamoto over a number of years titled "Mario 128" was shown off at Nintendo's Spaceworld 2000 trade show and was designed to showcase the GameCube's ability to utilize multiple AIs. The demo featured 128 Marios dismantling a pseudo-8 bit Mario sprite composed of several blocks by picking up and carrying them away. This project had a tumultuous development cycle with little to no details coming out over the years until 2007 when he revealed at a GDC Keynote that some parts of the project were utilized in two games he produced in the 2000s. The general concept and some other parts of Mario 128 were developed into Pikmin after Miyamoto asked his team to create an entirely new game that would be nothing like a sequel to a Mario game. As for the second game, the ability to warp the terrain seen in the tech demo as well as "different sizes of spherical items" influenced the free-form gravity and ability to walk around entire planets in Super Mario Galaxy.

There is a planetoid in the Space Junk Galaxy that looks a lot like the ship from Pikmin 2.

There is a planetoid in Buoy Base Galaxy that looks like a Poké Ball from the Pokémon series.