Originally, Boggy's three children (Groggy, Soggy and Moggy) were intended to appear in the game as part of a challenge called "Don't Bring Your Kids to Work Day", but the challenge was scrapped due to time constraints. In 2019, it was discovered that Soggy and Moggy not only had fully completed models in the game, but also AI that was reused from the Minjos in the game. They can appear in Banjoland Act 6 during the challenge "Home Improvements: Igloo Edition", where Soggy can be found running on top of Clanker, while Moggy can be found running on top of the display case, both far away from where the actual challenge takes place. It is currently unknown if Groggy is anywhere in the game.

In addition to the console Anniversary Collection, a Game Boy Advance counterpart was also planned. Originally named Mega Man Mania, the title would have included colored remakes of the five Mega Man games created for the Game Boy, along with a History section and artwork. The compilation was planned for a Q4 2004 release, but was repeatedly delayed, partly due to Capcom reportedly having difficulty in locating the source codes for most of the games, forcing them to recreate them from scratch. In January 2006, it was announced the compilation was being "placed on indefinite hold" as Capcom and gaming retailers began issuing pre-order refunds.

Following the game's release in 2013, it was featured on the "Clueless Gamer" segment on comedian Conan O'Brien's Conan talk show. During this segment, O'Brien was able to play as Superman with the "Flaming C" costume. "Flaming C" was a character co-created by O'Brien and DC Comics artist Bruce Timm, modeled loosely on O'Brien himself. When asked about the Flaming C skin in 2021, game director Ed Boon confirmed that a build of the game with the costume "exists somewhere", but the costume was never made publicly available.

If the game is forced to select a language other than English or French, an unused flag of Spain will be shown in the Options menu. However, no script exists for the Spanish language, so selecting it will do nothing.

A prototype version of the game was distributed on some pirated cartridges featuring stickers for the game Daffy Duck: The Marvin Missions. The level select screen uses an unused rendition of "Hooray for Hollywood", while the Game Over screen uses the "That's All Folks!" theme. This is unlike the final version, which instead reuses the introduction and main menu music respectively. Other differences include the language selection screen being absent, and lives counting from 0 instead of 1.

According to each game's original director Taisuke Kanasaki, D from Another Code: Two Memories, and Will White from Last Window: The Secret of Cape West, are both intended to share the same birthday as him.

Ports of Donkey Kong 3 were developed by Hudson Soft for Japanese personal computers such as the NEC PC-8801 and Sharp X1 in 1984. These versions of the game were different in that Stanley is unable to jump, protecting plants is removed from the game, and most notably, the game's levels tell an ambiguous but bizarre story. The level backgrounds display a vastly different setting from the original arcade version, having Donkey Kong and Stanley traveling down a highway, encountering aliens, going to outer space, and landing on an alien planet. In the NEC PC-8801 version's manual, Hudson Soft encouraged players to develop their own explanation of the game's story and share it with them via mail.

In addition to the console versions, a Nintendo DS version of Crash Landed was being developed by Renegade Kid, which was known for their polygonal 3D games on the handheld. In 2013, Nintendo World Report released a 3-minute video of a playable demo for the DS version. The game was a 3D platformer, much like Renegade Kid's other cancelled DS project Maximillian and the Rise of the Mutant Mudds.

In an early version of the game, a pie weapon was planned to be included that allowed Bubsy to throw pies at enemies. However, this weapon would ultimately only appear in the Game Boy version.

When the game was first announced, it was referred to as "Code Name: X", with the only hint towards its connection to the Persona series being that it was claimed to be the first mobile game in a "famous Japanese console game series" that had sold over ten million copies worldwide. While the game's aesthetics and music were both noted to be reminiscent of Persona 5, and the file names for the game's artwork on the website were referred to as "P5", an official connection to the series was not discovered until the binary code at the end of the game's reveal trailer was translated to "Persona 5X".

In the game's pre-release demonstration build, two files named "SET.DIB" and "SET1.DIB" can be found in the folders "SPRITES", "BACKUP" and "SPRTBKUP" (the last two of which are also included in the "SPRITES" folder). Both of these files contain sprites from Bubsy in Claws Encounters of the Furred Kind depicting Bubsy pouncing, gliding, falling, and landing, but also contain two sprites of him winking while posing with his arms behind his back, and him preparing to pounce.

The root of Bubsy 3D's disc contains a copy of the ending cutscene for the level "Escape from WooL.A." titled "DUMMY1.DAT". This file, and two additional copies of it named "DUMMY2.DAT" and "DUMMY3.DAT", are also present in the original US release of Syphon Filter.

At the end of the 8th season of Vote-a-Fling (an annual in-game event where players could vote for a girl from the game's "Phone Fling" mode to become a fully dateable girl), Honey was chosen as the winner for the season. Unlike past events however, the results were narrowly close between her and the second place winner Willow, with both characters frequently swapping first and second place before the voting closed. As a compromise, Sad Panda Studios announced that both Honey and Willow would be added one after the other as dateable girls.

In Chapter 4, the piano in the first sanctuary allows for a much more expansive range of notes than other in-game pianos. Accordingly, Susie and Ralsei have special reactions if the player inputs specific songs on it:

• Playing "Memory" results in Ralsei complementing it by comparing it to a lullaby.
• Playing "Your Best Friend" from Undertale results in Ralsei calling it "friendly and sweet," alluding to Flowey's introductory cutscene in that game.
• Playing "The Legend" flatters Ralsei, to which Susie responds by joking that Kris is flirting with him.
• Playing "Lost Girl" results in Susie wondering if she could learn it on guitar.
• Playing "Rouxls Kaard" results in Ralsei recognizing it as Rouxls' theme song; Susie then jokingly calls it the "theme of him getting his ass kicked."
• Playing "Heartache" (Toriel's boss theme in Undertale) causes Ralsei to describe it as "emotional" before Susie suggests playing it for Toriel.
• Playing "Undertale" results in Susie deriding the song as "crap."
• Playing "Dark Sanctuary" results in Susie pointing out that "Ralsei was humming it earlier."
• Playing the song on the Old Man's sheet music results in different responses depending on whether or not the player includes the octave switch: omitting it results in Susie & Ralsei commenting on its absence, while including it results in Susie commenting on how different it is.
• Playing the first four notes of "MEGALOVANIA" (Sans' boss theme from Undertale) results in the Annoying Dog abruptly running Kris over with the car from Cyber City's hidden alley in Chapter 2, which causes a smash to black before the game returns to normal. Attempting to replay the song results in Kris fumbling the fourth note.

Several other songs that produce reactions are transcribed unusually, and as such are more difficult to trigger if playing solely by ear:

• Playing A, D, E, F, D, D, C, D, B, A, D, E, D, C, D, D causes the pair to comment on the "annoying" nature of the melody.
• Playing "Don't Forget" (C, D, E, E, E, E, E, A, C, B, B, B, B, B, B, C, B, A, A, A, A, A, A, G, H, G, E, C) causes Susie to fall silent before calling the song "kinda cool."
• Playing "Spear of Justice" (E, D, B, C, A, B) results in Susie calling the song "majestic" before Ralsei suggests that the Old Man would enjoy it, referencing the song's nature as Spoiler:both Undyne and Gerson's leitmotif.
• Playing "Chopsticks" by Euphemia Allan, "Heart and Soul" by Frank Loesser & Hoagy Carmichael, or "You've Got a Friend in Me" by Randy Newman & Lyle Lovett (C, E, C, F, E, A, F, H, F, H, E) results in Susie scolding Kris for "messing around." Notably, all three of these are real-life, commercially released songs: the first two are common stock piano pieces, while the latter was recorded for the 1995 animated film Toy Story. Its inclusion likely references a series of comedic edits of the song posted to Tumblr by developer Toby Fox. One of these edits, "Friend inside Me", was previously the subject of tongue-in-cheek fan theories claiming that it would pertain to Chapter 3's hidden boss.

Eight games developed by Rare for the Game Boy Color and Game Boy Advance feature a recurring Easter egg: a crude drawing of a bovine eating a flower. Dubbed the "Rare Cow", it made its first known appearance in Conker's Pocket Tales in 1998, and last appeared in It's Mr. Pants in 2004.

The design of the Angels in the PlayStation version of the game was inspired by the clothes worn by Milla Jovovich's character Leelo in the 1997 film The Fifth Element. The film's costume designs were done by French designer Jean Paul Gaultier, who Shin Megami Tensei demon designer Kazuma Kaneko and SaGa series illustrator Tomomi Kobayashi had previously expressed admiration for.

Each version of the game has a costume called the Launcher with a themed design unique to each console, though all variants of them perform the same ability of shooting bullets while standing still:

• Star Launcher is exclusive to the Nintendo Switch version and is red akin to the Nintendo logo. Its bullets feature star effects, likely in reference to the Mario series.
• Blue Launcher is exclusive to the PlayStation 4 and PlayStation 5 versions and visually resembles a PS5 console. Its bullets feature effects with the PlayStation face button symbols.
• X Launcher is exclusive to the Xbox One and Xbox Series X|S versions and prominently features the Xbox logo. Its bullets feature green X's similar to the Xbox logo.
• Steam Launcher is exclusive to the PC/Windows version and features a large red valve on its back, in reference to Steam's creator Valve. Its bullets are also valve shaped.

Each version's Launcher costume was originally unlocked if save data from the game's demo was detected, but since the demo is no longer downloadable, the costumes can now only be unlocked by inputting a specific code on the title screen: L, R, L, R, L, L, R, R, Up, Down. The official Balan Wonderworld Twitter account initially posted a hint for players to figure out the code themselves, which could be solved by identifying which costume is found in the applicable world number.

The SNES version of Mortal Kombat was developed by Sculptured Software in the conservative state of Utah, an area where the backlash to the game's violent content was at its highest, and whose state legislature previously attempted to outlaw the original arcade version. According to the port's project director Jeff Peters, local children visiting the studio to ask about the game and its development also told their parents, who refused to associate with the developers and speculated that they were "drug dealers" and "Satan worshippers". He also recalled one programmer who asked the development team to lie to his family about what game he was working on.

On October 26, 2024, a special demo version of the game was given exclusively to YouTuber Matthew Patrick and livestreamed on his channel GTLive before he officially retired from making YouTube videos on that day. The end of the demo featured a special ending set within the Nugget Cave, referencing various theories and moments related to the series that Patrick covered on his webseries "Game Theory". Nugget then appears and declares him and his wife Stephanie Cordato to be "true friends of Nugget" while a sign saying "Farewell Matpat!" descends amongst a downpour of chicken nuggets.

The inclusion of the character Pauline was accidentally leaked through a piece of thumbnail artwork on Nintendo of Korea's website shortly after the game's announcement, but was quickly removed. Her inclusion would later be confirmed in a dedicated Nintendo Direct aired on June 18, 2025, where it was revealed that she was Spoiler:the true identity of the character Odd Rock.