Piranha Plant's side special, Poison Breath, seems to come from the Paper Mario series, specifically from the Putrid Piranhas from Paper Mario: The Thousand-Year Door. Piranha Plant's "bud" even changes color to match a Putrid Piranha's yellow and red color scheme during the attack. This would make Piranha Plant the only Mario series character to have a move derived from the Paper Mario series.

When Hero tries to use the spell Zoom indoors or under a ceiling in this game the Hero will instead bonk his head on the ceiling and the spell's teleportation will not work. This is in reference to the Dragon Quest games, where trying to do the same thing in the same situation will garner the same exact result.

The seemingly unique design for the Belmonts' Vampire Killer whip, with a metal chain, a morning star at the end, and the religious-looking crossguard, is actually very closely taken from two different sources: Castlevania: Lords of Shadow and the Pachinko game Castlevania: Erotic Violence.

According to Thierry Levastre, the game's lead graphic artist, a sequel was in development by Delphine Software, but was soon cancelled due to the poor reception of the first game. Concept art for the game was produced shortly after the game's production was cancelled.

The 2 Player mode found on the Game Boy version cannot be accessed through normal means and instead is accessible by playing the game on the Super Game Boy SNES adapter cartridge.

The SNES, Game Gear, and Game Boy versions of the game omit Colonel, Diesel, Leotsu, Nezu, and Auroch from the roster unlike in the Sega Genesis and Amiga versions, where in those versions have the character roster complete.

Both the Game Gear and Game Boy versions lack the Tournament Mode and digitized voice samples found in the console versions of the game.

Delphine Software originally pitched the idea of a basketball game to former NBA star Shaquille O'Neal, but O'Neal instead opted to pitch in the idea of a fighting game because he was a fan of Mortal Kombat. Delphine Software developed the video game using rotoscoping technology by filming Shaq and the stuntmen, then redesigning them to appear as characters in the game. A kung fu expert was then hired by Delphine Software to direct the action sequences to make the fighting aspects look more realistic.

In the living room of the Border House, to the left of the corkboard, there is a small, unmarked wall area that when hovered over will reveal a caption for a "Painting". Clicking it will instead cause April to walk to the adjacent right wall where the unseen painting is hung and comment:


During the cutscene "Vision in the Living Room" which is only played if April has chosen to not work the evening shift at the café, a shot of the painting depicting an abstract rendition of a woman's head can be seen. This painting appears to be a caricature of American actress Julianne Moore, who appeared one year prior to The Longest Journey's release in the 1998 film "The Big Lebowski" in the role of artist Maude Lebowski, suggesting that the painting may be a self-portrait.

Outside the Mercury Theatre, a poster can be found for a fictional film called "A Welsh Ghost Story" that April claims is "a classic", and is written and directed by Ragnar Tørnquist, the game's creator. This film was actually based on a real work-in-progress screenplay with the same tentative title by Tørnquist that would later be uploaded online in 2014 under the name "In the Dark Places".

In the living room of the Border House, hovering the mouse over the back part of the horizontal stand the TV is being held up on will display a prompt for a "Hidden button". Clicking it will cause the TV to play the first teaser trailer for The Longest Journey.

The Book of Secrets is a showcase of voice acting outtakes, unused music and concept art that can be unlocked by beating the game and is accessed from the title screen. However, there is a secret way to unlock it earlier on in the game.

Spoiler:In the hallway outside April's bedroom, a leaf from an Organic plastic plant can be collected. This leaf can then be used on the Flowerbed in The City Green, triggering an animation of April planting the leaf next to it which immediately sprouts a large flower. She will then comment about hearing a voice stating that a "Book of Secrets" was now open, unlocking the bonus content.

Flux Wildly, the game's deuteragonist, is named after the Flux Capacitor device from the Back to the Future series, in which Christopher Lloyd plays the character of Doc Brown.

Playing “Rhythm & Bruise” as Monty Mole will cause the character to sweat profusely and show a scared expression.

In battle, Susie's UltimatHeal move is tied to her magic stat like most other spells, and consequently recovers more HP should the player boost her stats through hacking. However, in the cutscene where she first demonstrates it to Kris, it is hard-coded to only heal 2 HP regardless of circumstance.

A Sega CD version of the game was at one point in development and was planned to be released by ReadySoft, but was soon cancelled due to the game being released on the Sega Saturn instead, despite the fact that the cancelled Sega CD version was still advertised in gaming magazines.

Near the end of the game, there's a bat that hugely resembles David Quesnelle, the game's art director.

By holding X or Y while using Samurai Fist, Jack can perform two secret animations that act as references to a scene from Episode XXXVI of the original series, where Jack and two Xiaolin monks battle and notice similarities between each other's skills:
•The first animation shows Jack performing the Water Beetle martial arts style.
•The second animation shows Jack turning towards the camera and performing the principal secret sign of the Xiaolin monks (a raised index finger and suppressed thumb).

According to the game's main designer/planner Takane Ohkubo in a 2013 ROM Cassette Disc in MELDAC liner notes, he was asked why he chose the game to be available on the Famicom console. He responded:

The bonus stage music that is used in Tapper is a slight variation of the song "Here Comes the King", a jingle written to promote the alcoholic beverage Budweiser which was the first sponsor of Tapper and featured the drink's logos plastered on multiple screens in the game. After Anheuser-Busch ended their sponsorship and the game was revised as "Root Beer Tapper", some song names needed to be changed to avoid legal trouble.

Leon's battle theme in the Battle Tower, composed by Undertale and Deltarune creator Toby Fox, appears to interpolate the track "A Baby Legend - The Baby is 2", from The Baby is You, a 2010 concept album by Fox based on the webcomic Homestuck. The choice of interpolation garnered attention for its strangeness by the standards of a Nintendo-affiliated game, as The Baby is You was a joke album about male pregnancy, made to poke fun at the Homestuck forum's rule against fanart surrounding the topic.