After collecting Whisper's Love, you can obtain a Rumrom in the Haunted House cellar called the Haunted Stone. Its description seems to refer to flying the Rocket to the Moon, but it's engraved with pictures of four arches leading up towards the Dragon. This image is actually referring to a scrapped area called "Dragon's Tail" that would have been used in a dream sequence triggered by Florence in the middle of the game, and later revisited in a cut ending by reflecting two mirrors at a gate to create a tunnel to the area. The Boy could see a transparent copy of his previous dream visit while there. Dragon's Tail can be accessed in a near-complete state with unused dialogue through the debug menu, and was not removed before release as the developers never expected players to find it. They considered adding Dragon's Tail to the 2019 re-release in either a re-worked form or as a DLC ending, but decided against it.

It was envisioned by designer Yoshiro Kimura and artist Kazuyuki Kurashima as a purgatory where souls from real life and the game world would meet before going to Heaven or Hell. It was inspired by books Kimura read at the time that made him feel there were "other layers to humanity than what we normally experience in reality", as well as a one-man stage play he put on while working at Squaresoft called "Mononoke", about a bullied boy who was transported to a similar purgatory. Dragon's Tail and its ending were cut when Kimura designed the Monster Catch system at the same time and thought the ideas that spawned from it were more interesting and fitting with the game's themes, and because he deemed the area too similar to a chapter from Osamu Tezuka's manga "Phoenix". Kimura recalled this as a stressful change as all the assets for the new ending had to be built out of clay and then imported into the game.

Dragon's Tail also adds more backstory to a low-key item in the final game called the White-Feathered Arrow. Through interactions with Bilby, the Minister, and two documents in his bedroom, it's revealed that this item Spoiler:was shot in the air as part of a ritual to randomly select a citizen to slay the Dragon. That person was sealed inside the Hero's armor, a cursed relic, and will continuously chase and fight monsters until they die of old age. As the game parodies contemporary RPGs like Dragon Quest, it's theorized that the White-Feathered Arrow is based on the cursor used to name your player character in that series. In the dream sequence, the Boy discovers a crying naked boy who will follow him through the arches into the house at the end of the area. Inside is Spoiler:Gramby's house, where it's revealed that the naked boy is not only Gramby's presumed dead grandson, but also the Hero who is destined to atone for killing monsters by healing them all. A long line of monsters and people from various time periods forms outside the house that can be talked to, and talking to Florence at the end of the line will end the dream sequence. In unused cutscenes and the unused ending, Spoiler:the naked boy slowly evolves into the Dragon as he heals more monsters, and is eventually killed by the Hero in the armor who he acknowledges is himself, presumably leading to the last scene in the real-world in the final game.

On the cover of both versions of MySims Kingdom, King Roland is depicted as having light blue eyes. While this is reflected in the Wii version, the DS version instead depicts him with grey eyes in-game.

Driving for a certain period of time without crashing will make Konami's mascot Konami Man appear, awarding the player 3000 points in the arcade version and 1000 points in the NES/Famicom version.

The human characters featured in the MSX and PC versions were changed to penguins in the Famicom version. This decision seems to have been made so the game could compete with other popular penguin games released in Japan at the time including Penguin Land, Antarctic Adventure, and Pengo.

Originally, The End was supposed to have a boss battle in the same fashion as the other Titans from the main story, but it was changed into a shoot-'em-up style battle due to the approaching deadline during development. It is possible however that the revamped boss battle against The End in The Final Horizons DLC Expansion was meant to revisit the original plan, as it more closely resembles the Titan boss fights than The End's fight in the base game.

As part of a wave of risque video game magazine advertising throughout the mid-1990's, Battlecruiser 3000AD's publisher GameTek promoted the game in the United Kingdom with ads featuring glamour model Joanne Guest wearing only high heel boots, a brassiere, and straddling a stool while hiding her genitalia behind a copy of the game. Four variants of this ad circulated throughout 1996 and 1997, with the variant depending on the age demographic that a magazine was aiming for as well as being affected by later censorship rulings. Initially, more "laddish" magazines aimed at British men in their late 20's featured a version of the ad with the added caption "she really wants it", with another separate variant printing the word "really" in a larger font size. The publicity from these three ads resulted in several complaints being filed to the UK's Advertising Standards Authority, who eventually cracked down on several game and magazine publishers for their vetting regulations for ads, including the Battlecruiser 3000AD ad. A censored version of the ad replaced the "she really wants it" caption with the message "Censored by Publisher", and featured knickers airbrushed onto the existing photo of Guest. Around the same time, THQ ran a parody of the ad depicting a fully-clothed elderly woman mimicking Guest's exact pose (even down to chewing on the same finger), but with the game's box art replaced with THQ's logo.

The graphics for the Neutral Zone are made up of bits and bytes of the actual program code for Yars' Revenge, laid out vertically, and counter-scrolling over each other. The game's creator Howard Scott Warshaw recalled in an interview with Digital Press that Atari feared showing the game's code on-screen would be a potential copyright violation, but Warshaw explained to them that "besides the scrolling, there was some X-Y and random color processing being done to it" to prevent the raw code from being displayed, stating that "if somebody could get the code from that, then they deserved it!" This same technique was employed by Retro Studios to create static noise textures during the development of the Nintendo GameCube game Metroid Prime.

At one point when playing the Grand Metropolis stage as Team Chaotix, Vector will say "Boy, it doesn't look good.", after which Espio responds saying "I'll handle it". The closed captions however instead say "Leave this to me!".

Graphics for an unused ammonite enemy can be found in the game's files.

The game contains data for an unused saber-tooth cat enemy. It has idle, turning, walking, and running animations, as well as hurt and dying animations.

According to former Nintendo character designer Takaya Imamura, Wolf O'Donnell was inspired by his grandfather, who he described as being a "bad man".

The copyright notice in the sound test of OutRun for the Commodore 64 mistakenly lists the game as having come out in 1941.

There are four unused music tracks in the game. Two of them were planned to be character themes for Makoto and T.O.B.O.R., and the other two were planned to be racetrack themes for Pinball Canyon and Dr. F's Daredevil Drive.

If you beat Story Mode and then play through it again, the captions for Jonathan's response to Dio kicking his dog Danny in the jaw are slightly altered. Instead of reading "何をするんだ" ("What the hell are you doing?!"), it will now read "何をするだ" ("What the hell you doing!?"), which is identical in meaning, but omits the hiragana character "ん". The typo in the second playthrough is deliberate and references a mistake made in that scene when it was published in the manga's original 1987 print run. This typo stuck around in reprints for almost 15 years, becoming a meme among Japanese fans for making the intended line sound like a "country-like scream", until it was finally corrected in a paperback release in 2002.

"Meatophobia", the ominous background music that plays when approaching Pillar John and activating Pizza Time, features a timestretched version of the same hip-hop orchestral hit sample used in the Small Graffiti sound effect from Jet Set Radio.

There are two unused pieces of headgear in the files of the original Nintendogs games: a chonmage wig (a Japanese male ponytail haircut worn by samurais in the Edo period to hold their helmets in place), and an afro wig. The chonmage has an unused description found in the Japanese version of the games and had all of its assets in the international releases replaced with the data for the Rainbow Wig. The afro on the other hand was finished enough that you can use cheat codes to make a dog wear it, but it does not have any leftover text or item attributes that let it be obtained as an item. It may have been cut from the games late into development due to concerns over racial offense and replaced with the Rainbow Wig, which has a very similar appearance to the afro, but with a rainbow-colored texture instead of one resembling black hair.

A sequel to MySims Agents called MySims Agents 2 was planned, but was ultimately shelved in Fall 2009. Years later on May 12, 2023, designer Brian Kaiser shared an old completed story outline for the game on his Twitter account. Based on the outline, the plot would have revolved around the player investigating a series of strange events involving an unknown energy source (later revealed to be seeping through portals from the Nightmare Realm), all while contending with the new S.P.A. director Morgan (a reworked version of the scrapped character Vice Admiral Morgan from MySims Kingdom) and her advisors Dragomir and Svetlana (reused from MySims SkyHeroes), who has shut down several branches of the agency as part of "restructuring" and captured Walker after he began to investigate them. Several characters from the original game would have returned, with Roxie Road, Jenny, Dr. F, Buddy, and Vic Vector all being part of the player's team as they solve cases all over the globe. While full gameplay details are unknown (aside from a new grapple hook mechanic), some pieces of concept art have been released since, such as designs for Morgan's various monster forms.

JoJo's Bizarre Adventure: Heritage for the Future was originally released as JoJo's Venture in December 1998. This version suffered from a rushed development, reflected by the abundance of unused assets in its code, including both finished and unfinished sprites for various attacks, cutscenes, and HUD elements. An updated version would come out eight months later, this time using the series' full title and adding the Heritage for the Future subtitle. A significant chunk of the unused assets in JoJo's Venture would be polished up and incorporated in this newer version.