Captain Commando is commonly believed to be set in the future of the Street Fighter universe due to its numerous references to another series set in the same universe, Final Fight. Specific examples of this include Captain Commando taking place in Metro City (a recurring location from both Final Fight and Street Fighter) and Ginzu being trained in the fictional Bushinryu Ninjutsu style of fighting used by Guy. The latter connection would be elaborated on by Street Fighter 6 director Takayuki Nakayama, who revealed that Ginzu's father Gou (a character who had previously only appeared in concept art) would eventually succeed Guy as the 40th Bushinryu Grandmaster, with Ginzu eventually becoming the 41st Grandmaster.

Gou would later make his official debut in Street Fighter 6's World Tour mode during Kimberly's second memory dialogue, where she mentions how she was easily beaten by him. His appearance here depicts him wearing a purple version of Guy's Bushinryu outfit (similar to Ginzu's uniform) and holding a katana similar to Ginzu's signature weapon Lightning Light. Another reference in World Tour mode comes in the form of Carol, one of the minor enemies from Captain Commando appearing as an opponent during the "Fighty Mighty" mission quest. Her appearance is loosely based on her in-game sprite, wearing a blue tank top and pants as well as having pink hair (though here it's depicted as being straight rather than a ponytail), and her dialogue upon being beaten alludes to her role as a criminal in the original game: "Reminds me of old times, back when I was involved in some...slightly unscrupulous business."

However, there is one detail that brings this theory into question. In the Character Reference section of the Street Fighter V Shadaloo Combat Research Institute website, the profile for Yuta Homura mentions that he can clear Captain Commando using Mack the Knife (under his Japanese name Jenetty, "ジェネティー") with a single credit. The game is not mentioned by name though, and is instead referred to as an unspecified "beat'em up action game".

Within the game's data is an unused placeholder Masterpiece banner for the original Super Smash Bros. The banner is located in the game's files alongside those for the other Masterpieces, which together with its filename, "soft_50_SuperSmashBros.nut", indicates that it is meant to represent the game rather than being a failsafe. Furthermore, the placeholder nature of the graphic and the lack of any other assets related to it indicate that the demo was removed relatively early into development. As no Nintendo 64 games are featured as Masterpieces in Super Smash Bros. for Wii U, this would have made Super Smash Bros. the only game to hold this distinction.

Nitrome began development of Mouse Work before the Nintendo Switch 2's mouse functionality was officially revealed, with the concept being based on industry rumors and a tease of the feature from the system's official announcement video. As they hadn't received a software development kit from Nintendo, they instead used Joy-Cons duct-taped to computer mouses to prototype and develop the game. Nitrome founder Mat Annal attributed the company's experience in making browser games with allowing them to develop the game so rapidly.

Prehistoric Kingdom had its origins in a fan project originally titled Jurassic Park: Operations, an attempt at an unofficial successor to Jurassic Park: Operation Genesis. The project was later rebranded to Jurassic Genesis, presumably to avoid copyright issues. Nonetheless, the project was stifled by accusations that the game's lead, Will Loudermill, stole game assets from various third party sources, and that the game's co-lead, Matt Willson, allegedly attempted to auction the project off to the highest bidder through PayPal. It was these controversies with the project's management that prompted a handful of the development team to break off and create their own prehistoric-themed park building game, which became Prehistoric Kingdom.

The Special Flag item originally found in the Namco game Rally-X has since become a recurring symbol used in games developed and/or published by Bandai Namco, including Xevious, Gaplus, Tinkle Pit, Tales of Phantasia, and the Super Smash Bros. series among others.

Schedule I has been noted to have many similarities to the Drug Dealer Simulator series, to the point that the latter games' publisher Movie Games SA launched an investigation into potential intellectual property infringement in in April 2025 regarding the gameplay mechanics and UI designs of the two games. While the developer behind Schedule I, named Tyler, confirmed that he had been contacted by Movie Games, there had been no further communication between the two, nor had any legal action been taken. Despite this, the situation prompted backlash from players, who responded by leaving negative reviews on the Drug Dealer Simulator games' Steam pages.

In a post-release interview with Game Informer, AlphaDream producer Yoshihiko Maekawa and Nintendo producer Akira Otani stated that the decision to develop the game for the Nintendo 3DS (then in its twilight as an incumbent platform) instead of the Nintendo Switch was due to the former allowing the developers to carry over the original game's dual-screen gameplay, as well as due to timing where they could build off existing assets. They also cited numerous factors behind AlphaDream's decision to remake the third game in the sub-series directly after the first game (thus skipping the second game, Mario & Luigi: Partners in Time). According to Otani and AlphaDream director Shunsuke Kobayashi, the biggest factor was that Bowser's Inside Story was "the best received title in the series", with other reasons including a desire to explore the father-son relationship between Bowser and Bowser Jr. in Bowser Jr.'s Journey and the ability to carry on Fawful's subplot from the Bowser's Minions mode in Mario & Luigi: Superstar Saga + Bowser's Minions. Kobayashi described the process of developing the new mode as "really fun for us" thanks to the ability to emphasize the comedic aspects of the game's cast, with Otani further highlighting the opportunity to tell a kid-friendly story about a protagonist rebounding from hitting rock bottom.

Terrence Suave, a minor background character seen only on portraits in the Henry Stickmin games "Infiltrating the Airship" and "Completing the Mission", is named in reference to the "Terry Suave" disguise from the 2002 film The Master of Disguise. Series creator PuffballsUnited revealed this in a live developer commentary of the game on Twitch, because he thought nobody got the reference.

An unused post-credits cutscene was discovered on a late beta build of the game dated to January 28, 2013, three months before the retail release. The cutscene re-contextualizes Far Cry 3: Blood Dragon as being "a game within a game", featuring a younger Vaas staring at TV static, and is seemingly connected to an achievement in the retail release titled "The Drug of the Nation". The achievement is unlocked by turning off all 32 TV sets throughout the game in order to "Decrypt the Hidden Message", though it's never revealed what this is. Prior to this discovery, some players theorized that the hidden message was actually telling players they wasted their time turning off TVs in a video game while staring at a TV expecting a reward, hence TVs being "the drug of the nation", and calling back to a popular monologue by Vaas from Far Cry 3 about the definition of insanity.

In the retail release, Dr. Earnhardt's backstory was very briefly acknowledged within his character entry in the Handbook, in which he sailed to the Rook Islands after his two-year old daughter died falling out of a window in their London flat. An unused cutscene left in the game files shows that Dr. Earnhardt would have personally revealed his backstory shortly after being introduced to Liza by Jason, following her rescue. Dr. Earnhardt specifies that installation work was being done, while in the retail release, no context is provided for how the tragedy occurred.

After rescuing Knuckles in the original Sonic Generations, he asked Classic Sonic if he had suddenly gained weight, leading him to insecurely rub his belly. In Sonic X Shadow Generations, this scene was rewritten and re-recorded to instead have Knuckles ask if he knew where the rest of Angel Island is. However, the original animation where Classic Sonic rubs his stomach was left intact, appearing to imply that he ate Angel Island.

A year after the release of Mario Kart 8, a hip-hop dance known as the "dab" would gain prominence in mainstream culture, becoming a popular internet meme. Mario fans later noticed that at certain angles, one of Donkey Kong's Jump Boost animations in Mario Kart 8 coincidentally resembled a dab, with Donkey Kong holding his head down and stretching out one of his arms, but keeping his other hand close to his head. In Mario Kart World, this animation returns in a different context. While Donkey Kong now faces his head forwards while doing the animation, straying away from dabbing, he also stretches out both arms, making the similarity to dabbing more prominent overall.

In the Side Order DLC expansion, the noises made by the bosses Asynchronous Rondo and Pinging Marciale are actually distorted clips of the Off the Hook songs "Ebb & Flow" and "Fly Octo Fly" respectively.

The Four Horsemen's nickname, Ultrabox, is a play on the English new wave band Ultravox, of whom series creator Hideo Kojima is a longtime fan.

The game was originally going to have twenty songs, but only nineteen were included in the final game. According to an article from 1UP.com, the scrapped song was "Livin' la Vida Loca" by Ricky Martin. This would be confirmed years later by video game journalist Liam Robertson in a video detailing the history of the game and its Japanese counterpart Osu! Tatakae! Ouendan. According to the video, the song was cut due to licensing issues later in development, with UI programmer Robert Ota Dieterich stating it was intended to be used in the game's second level before being replaced by "Makes No Difference" by Sum 41.

In 2013, Renegade Kid co-founder Jools Watsham posted a 3D-compatible mock-up depicting a hypothetical Nintendo 3DS port of Virtual Boy Wario Land with full-color graphics. While a note in the mockup claimed that it was just for fun, Watsham revealed in an IGN interview three years later that he had presented it to Nintendo with the intent of spurring interest in such a project, further offering to port the entire Virtual Boy library if Nintendo desired. However, he never got a response back; Watsham speculated that he was ghosted due to lingering embarrassment over the Virtual Boy's commercial failure.

According to programmer Sertif in a reply to a now-deleted tweet, Gustavo's steed Brick the rat is intended to be female. Composer ClascyJitto corroborated this and assumed that the reason fans did not know this beforehand was because it was not overtly stated in the game.

A limited edition of the game was released in North America and Europe that came bundled with an exclusive novelty controller shaped like the Wu-Tang Clan's logo. It was noted for being cheap and lightweight, featuring all of the buttons on the original PlayStation controller, but lacking the vibration and the analog sticks featured on the DualShock controller.

After getting the HEV Suit at the start of the game, Gordon Freeman can open his work locker nearby and collect a battery to power up the suit. A picture of a newborn baby can also be found in the locker, but contrary to popular belief, this is not his child. The game's manual includes Freeman's Black Mesa job acceptance letter, which reveals that he is "unmarried and without dependents". The real identity of the baby is Isabel Teasley, the daughter of Half-Life artists Harry Teasley and Yatsze Mark born in January 1998. Teasley originally hid the picture on a broken desk in a ruined office on a completely different map as a personal Easter egg. However, level designer John Guthrie discovered this, and decided to replace a pin-up poster Teasley put in the locker with the picture. Teasley recalled the birth of his daughter as a very difficult time, as she was born with a developmental disability and needed to be fed through a tube in her stomach every two hours, while the last year of Half-Life's development when she was born was dominated by crunch work. Series writer Marc Laidlaw stated in an email to a fan in 2006 that the writing team had no reason to elaborate on who the child is supposed to be in-game, but because the intention of putting the picture in the locker was to show something that had personal significance to Freeman, he suggested she could probably be his niece.

Marketing materials produced by Nintendo for Conker's Bad Fur Day, as well as the back of the game's box, went out of their way to refer to the game's alcoholic protagonist as having just turned 21 years old. However, according to a pitch document for the unmade sequel Conker's Other Bad Day, director Chris Seavor intended for Conker to have been underaged during the original game's plot, and the sequel would have taken place after he had turned 17-18 years old.