The longtime fan term "Eeveelution", which refers to the various evolutions of the Pokémon Eevee, first appeared in the 2001 Nintendo Power Player's Guide for Pokémon Stadium 2. It was first used within an official game in 2008's Pokémon Ranger: Shadows of Almia.

The American release of Pokémon Stadium 2 has a two-toned cartridge, with the front being gold-colored and the back being silver-colored in line with the background of the game's box art. This is a reference to [[Pokémon Gold Version|Pokémon Gold and Pokémon Silver Version|Pokémon Silver, which could transfer information to the game using the Nintendo 64 Transfer Pak.

The American release of the game has an exclusive spelling error, where two Ninetales cards are mistakenly spelled "Ninetails." However, Ninetales is spelled correctly in one of the cards' description texts. This was fixed in the European release.

Within the data of Chapters 2, 3, and 4 is a variable for the TP meter titled "shit," which is set to 1 whenever the global.tensionselect variable (used to indicate the amount of TP required to cast the currently selected spell) is uninitialized. Under these conditions, the game is programmed to play the recurring splat soundbyte. In Chapter 5, this variable is renamed "toylet." The purpose behind this variable is to bypass an issue where Game Maker crashes when trying to call a variable that hasn't been initialized yet; consequently, the "shit"/"toylet" variable serves as a means of highlighting such errors without disrupting gameplay.

General Skarr's gardener alternate costume is based upon his design from the season 5 episode "Herbicidal Maniac", while his default appearance is based upon his original design from Evil Con Carne, the sister series to The Grim Adventures of Billy & Mandy, where he originated.

Shinobu Kamizono's model from Gal*Gun: Double Peace can be found within the game files, likely having been ported over for testing purposes. Comparing it to her model in Gal*Gun 2 reveals various subtle changes made to the character models in the game:

• Due to shoes now being treated as a separate piece of clothing, the "Body" models are now barefoot by default.
• Skirts and ties were made looser in order to show off the cloth physics.
• "Face" models are simplified, being flatter and smoother with rounder ears.
• The overall polycount of the models are generally lower than before.

The first puzzle to be implemented into the game involved a scenario where one player had to walk through a tunnel while the other player opened doors to let the player in the tunnel through. According to co-designer Jacob Strasser, this was later removed from the game after the developers decided that the puzzle was "un-fun".

If you remain idle on the character select screen without selecting a character for roughly ten seconds, Dr. Crygor will get out his phone and call Penny for a brief chat.

According to director Shinya Hiratake, Wingo's character design was inspired by a known habit of crows to collect shiny objects, while his massive size was inspired by the Roc, a Middle Eastern mythical bird of prey popularized in Arabic fairy tales including two in the collection "One Thousand and One Nights".

The international release of Pokémon Trading Card Game changed Jynx's artwork from black to purple. This was likely done in an attempt to distance the character from allegations of racism after complaints arose that her original design appeared similar to blackface caricatures. Years later in 2014, the artwork was changed again for the Virtual Console re-release of the game, making Jynx a lighter shade of purple.

In the initial release of Chapter 5, due to a programming oversight, Jackenstein would not appear in Castle Town if the player had killed any Titan Spawn in Chapter 4. This was fixed in the v0.0.250 patch.

Within the game's data is an image depicting the game's developer Andy Land (via composited stock assets) flipping off the viewer while shouting "FUCK YOU DECOMPILERS." For unknown reasons, the image appears twice in the game's files, with unique IDs for each copy (spr44154 and spr44316).

Captain Britain was a character who Marvel pushed to be included within the PlayStation Portable verison of the game, but he was scrapped for unknown reasons. A model was created and rigged based upon his design from the 2005 limited comic miniseries "The Ultimates 2", but was never used. Despite this, Captain Britain makes a cameo appearance in the game's good ending, if the player decides to locate an antidote for Namor.

Within the data for Chapter 4 is an unused minigame for the Mike Zone. This minigame is a Flappy Bird clone based on Small Mike's "Applause" attack which uses the microphone mechanic to replicate the mobile game's use of tap controls. Points are scored based on the amount of time the player spends in a round rather than the amount of microphones (which fill in for Flappy Bird's pipes) that they pass. The speed of the minigame increases as it goes on, and microphones eventually start appearing at visible angles rather than straight up and down. Given the minigame's roots in one of Small Mike's attacks and that the minigame uses the same high score counter as Battat (Small Mike's minigame in the PC and console releases), it's likely that the former was eventually reconfigured into the latter.

According to composers Hirokazu Tanaka and Keiichi Suzuki, the eclectic soundtracks for both EarthBound Beginnings and EarthBound were influenced by a large catalog of popular music, including the following albums:

• The Beach Boys - Smiley Smile (and the infamous long-unfinished original version Smile) (1967)
• Van Dyke Parks - Song Cycle (1967)
• John Lennon - John Lennon/Plastic Ono Band (1970)
• Return to Forever - No Mystery (1975)
• Stackridge - Mr. Mick (1976)
• Yabby U - King Tubby's Prophesy of Dub (1976)
• Randy Newman - Little Criminals (1977)
• Godley & Creme - Consequences (1977)
• Machito Orchestra & Lalo Rodríguez - Fireworks (1977)
• Weather Report - 8:30 (1979)
• Andy Partridge - Take Away / The Lure of Salvage (1980)
• Prince and the Revolution - Around the World in a Day (1985)
• Prince - Sign o' the Times (1987)
• Brian Wilson - Brian Wilson (1988)
• Randy Newman - Land of Dreams (1988)
• Hal Willner & Various Artists - Stay Awake: Various Interpretations of Music from Vintage Disney Films (1988)
• Lalo Rodríguez - Un Nuevo Despertar (1988)
• A Tribe Called Quest - People's Instinctive Travels and the Paths of Rhythm (1990)
• Frank Zappa - Make a Jazz Noise Here (1991)
• My Bloody Valentine - Loveless (1991)

They also cited as influences the works of Irish producer David Cunningham, and English composer Michael Nyman, who created an arrangement of "Eight Melodies" for the 1989 Mother soundtrack album. Tanaka also cited the 1973 album Sentimental Street by the band Hachimitsu-Pie, which Suzuki was a member of.

According to former game director Isaac Christopherson in a Twitter Q&A following the release of Chapter 5, the Outimals, Chum Chompkins, and Giblet were brand new characters created for the chapter and were not part of his initial outline. In comparison, Lily Lovebraids had early concept art made prior to his departure, wherein she was depicted with two large braids that she walked with in a similar manner to the character Doctor Octopus from Spider-Man. Despite this, Lily wasn't included in the outline either, as Christopherson wasn't sure if she could be fit into the story of chapter 5.

Of the 50 Landmarks featured in game, some are based on locations from other Marvel properties (prior to the introduction of the Marvel Cinematic Universe or before Marvel obtained film and TV adaption rights). These landmarks include:

• Goodman, Lieber, Kurtzberg & Book (She-Hulk)
• Nelson & Murdock, Attorneys at Law (Daredevil)
• Stark Tower (Iron Man)
• Baxter Building (Fantastic Four)
• Sanctum Sanctorum (Doctor Strange)
• Daily Bugle (Spider-Man)
• Latverian Embassy (Doctor Doom)

The Hulkbuster Iron Man skin exclusive to the Xbox 360 and PlayStation 3 versions is normally available via achieving Threat Level 9 in the hub world and beating the Hulkbuster miniboss. Alternatively, it can also be unlocked if save data from the 2008 Iron Man game is detected on the memory card/hard drive. The achievements unlocked from this, "Shell Head" and "World War Hulk", reference a recurring nickname for Iron Man and a 2007 Marvel comic book miniseries respectively.