Yoshi was originally planned to appear in Super Mario Galaxy, and was featured in proposal documents for the game from 2005. However, he was removed due to the developers thinking that "it would've been too much all at once." They said that, "if you're going to put Yoshi in a game, he has to be a main element, but [Super Mario Galaxy] had spherical land forms and gravity shifts and lots of elements that were entirely new" and, "Even if we had used him, we might have only been able to use him on a single stage."

Despite this, it was decided early on in the development of Super Mario Galaxy 2 to include Yoshi in the game, because his control scheme could act as a new main element of a new game and a "multiplication" of the elements from the previous game. The Wiimote controls for Yoshi were also formed early in development, with Shigeru Miyamoto taking pride in the tongue pulling mechanic used for eating fruit, fighting enemies and flipping switches, saying it "isn’t like anything you've ever experienced before." The rest of Yoshi's controls were shaped based on internal feedback from "everybody's love" for Yoshi, listing the development team, Mario Club Inc., and Nintendo of America as primary influencers for what the image of Yoshi should be, but tried to avoid making him too powerful. The developers also had composer Kazumi Totaka record new voice lines for Yoshi for the first time in ten years, and was reported as feeling "a little uneasy" and worried that Yoshi would sound like he had aged, but these were not concerns to them and the recordings were used in the game.

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.