The games' most prominent subplot focuses on the conflict between Team Aqua and Team Magma in their efforts to gain control of the legendary Pokémon Kyogre and Groudon to change the climate in response to the effect of humans on the environment in order to create expanded environments for sea and land Pokémon respectively. This subplot may draw direct inspiration from a real life controversy that was a prominent issue in Japan at the time of the games' development and continues to be. The Isahaya Bay land reclamation project on the Japanese island of Kyūshū, which the Hoenn region is based on, aimed to expand the available farmland in one of Japan's last wetland habitats. This lead to fierce political conflict from environmentalists who argued that the project would cause long-term damage to the wetlands and the marine ecosystem of the area through agricultural runoff released into the sea, and from reclamation activists who argued that Kyūshū needed the land as Japan has very little arable land already and needs to produce enough food to feed its increasing population and keep up with rapid industrialization. The concept of Team Aqua and Team Magma draw striking parallels to each side of this issue (i.e. reclaiming land where there used to be sea and protesting to reclaim sea where there is now land) while being written as cultic villains akin to Team Rocket from past games without distinct arguments to their positions, causing these parallels to be obscured and emphasizing the personal gain of expanding or reducing land for the sake of certain land or sea Pokémon to be won out from the conflict with little to no regard for humanity.

In Pokémon Emerald, the unified story featuring Kyogre and Groudon both being pacified by the presence of Rayquaza, a Pokémon heralding from the sky which in many religions and mythologies is where powerful gods and deities live, hints that a divine compromise between civilization and nature is the necessary solution, with how Hoenn is presented in the final game through the coexistence of different environments, humans and Pokémon being the result. This suggests that the preservation of Isahaya Bay while allowing for land reclamation elsewhere is the compromise this subplot is trying to get across.

At any time during a battle when the player is selecting a command, pressing Right/Right/Left/Left/Up/Down/Up/Down/Right/Left will play a voice clip of Vyse sighing and remove his goggle for the rest of the battle. This is a purely cosmetic change and has no effect on battles.

Exclusive to the GameCube re-release is a set of unlockable bonus content colloquially referred to by fans as "The Three Secrets". The requirements for earning this content is as follows:
•All discoveries need to be found and reported
•The number of opened Treasure Chests must be at 90% or above
•All Crew Members must be acquired
•All Moonfish need to be captured and given to Maria's bird Piccolo
•All Wanted Battle bounties must be found, beaten, and reported
•Beat all four optional battles with Piastol and finish her story
•Defeat over 2500 enemies
•Defeat all four Sky beasts
•Win 12 non-story Ship Battles

Upon meeting this criteria, The Three Secrets can then be acquired:
1. The Mystery Merchant will now sell the Sky Fang sword to Vyse.
2. A secret discovery can be found on a peak of a rocky overpass in High Sky just outside of Sailor's Island. This discovery is a Golden Hamachou, and does not appear in the Journal after it is found.
3. At Crescent Isle, a hidden boss Spoiler:Vigoro, who in the GameCube version became an Air Pirate following his third encounter with the main characters can be fought.

Series producer Kensuke Tanabe stated, in an interview with The Verge, that Zip Lash would be the final game in the franchise if it wasn’t well-recognized or didn’t sell well. This became the case as the game was a critical and commercial failure, resulting in the series’ dormancy. Chibi-Robo!’s developer Skip Ltd. has also not released any new games since.

On the Continue screen, Fox can be seen standing alongside a grid display showing off the 3D model of an Arwing, which can be interacted with.

Controls:
•D-Pad = Rotates the model; pressing or holding down in one direction will cause it to move faster; doing so in the opposite direction will cause it to slow down; doing so in a perpendicular direction (i.e. pressing either left/right and then pressing either up/down, or vice versa) will not affect the speed of the model.
•X button = Stops the model's movement; moving with the D-Pad resumes it.
•L and R buttons = Zooms in and zooms out the model respectively.
•A button = Holding this button triggers a "drawing" mode where a still image of the frame where the render last appeared will trail behind it infinitely with each succeeding frame; this effect is similar to the "trailing/ghosting" glitch that can occur when dragging windows or dialog boxes on older computer operating systems.
•Plugging in a second controller = Every button except for L, R, X and A, will let you scroll through numerous models of enemies found throughout the game.

Near the halfway point of Dream 2: The Flower Garden, if you use the Bee to fly over a large body of water, you will land on a platform that is blocked off by a small tunnel that can only be accessed while riding the Lizard. Flying back over to the other side will spawn a unique enemy that does not appear anywhere else in the game: a blue rabbit that throws green easter eggs and will charge at you if you walk too close to it.

On the title screen, pressing Up/Select/Left/Right/A/A/B will cause a level select option called "Dream Select" to appear below the Start option. After scrolling down to the Dream Select option, pressing the A button will play a short tone that indicates one additional level has been selected. For example, if you press the A button 3 times, you will hear 3 chimes, and then pressing the Start button will take you to the 4th level in the game.

One of Hideo Kojima's early ideas for the game's ending was to have Snake and Otacon turn themselves in to the United Nations for breaking the law (presumably for the crimes they committed operating as Philantropy during Metal Gear Solid 2: Sons of Liberty), and be convicted and executed. The rest of the developers reacted negatively to this ending, which resulted in Kojima changing it. However, it's possible a remnant of this ending was left behind in the form of the game's end credits theme, a cover of "Here's to You", originally written for the 1971 Italian docudrama film "Sacco & Vanzetti". Both the song and film center on two Italian anarchists who migrated to the United States in 1908, and in 1920 were convicted and sentenced to death after being accused of murdering two people during an armed robbery. The original 1971 recording of the song would later be used as the opening theme to Metal Gear Solid V: Ground Zeroes.

The microgame "Wario Wear" has unused graphics of a naked Wario, whereas the released version features him wearing an undershirt and underpants at the start of the microgame.

In Warlock Zone IV, a villager will reference the Konami Code by telling the player:

It was previously believed that the Z Saber Battle Chip could only be accessed by trading it into the game from Mega Man Zero 3, of which each copy of the game had only one copy of the chip. However, in 2022, an easier way to obtain the chip was discovered by entering the following hidden code at the Number Trader: 72794137. This code also works in the Japanese version of the game, causing its existence to baffle players as it has never been released in any of the game's official strategy guides. It's possible that the code was intended to be used during development as an easier way to access the chip without having to trade it across games, and that it was never meant to be found by players.

According to The Walking Dead's co-creator and writer Robert Kirkman, he became interested in making a game based on the comic after playing Strong Bad's Cool Game for Attractive People. Sometime later, Telltale Games would successfully pitch their idea of a Walking Dead game to him:

If you let the Master's Army destroy Necropolis, a ghoul refugee who survived the invasion can be found hiding behind a bookcase with dialogue talking about the invasion, while also mentioning that the attacking super mutants had "some steam trucks". These steam trucks are the only working mechanically propelled vehicles mentioned in the game, and are only mentioned in this Fallout game.

In the eighth installment of the Fallout Bible, Fallout 2 developer Chris Avellone revealed that steam trucks were planned for Fallout, but they were only mentioned in passing for "art reasons and gameplay reasons" and that it may have been an "ugly-looking vehicle".

GoldenEye 007 was originally planned to be included in the collection, even going so far as having a "Rare Revealed" video focused on the making of the game produced for it, but was scrapped due to licensing issues. This video would later be leaked online in 2019 by a former Rare employee.

The game was originally developed as sequel to the Double Dragon fighting game on the Neo Geo, however because of "different reasons" the game was turned into its own IP, becoming a tribute to Double Dragon instead of an official game in the series.

Early footage shows Super Kurara having her classic design. In the final game, her appearance was changed to be that of a maid.

The intro to the track "WELCOME TO THE CITY" interpolates the chorus melody to "74", a 2018 song performed by J-pop singer Itoki Hana that Toby Fox had previously composed and provided guest vocals for.

"Hatman" is a recurring crude caricature of a Viacom New Media higher-up that the developers hated. Originating as paint graffiti of the person on a wall whose identity was disguised by putting a top hat on it, it soon made hidden appearances in the rest of the developer's output as an obligatory easter egg. The earliest known Hatman easter egg made for a game was a short CG animation for the game Beavis and Butt-Head in Virtual Stupidity.

On the End Credits screen, entering one of the following four codes without the quotation marks, "BOIDUTS", "YNNIF", "SKCUS", or "NAMTAH", will trigger one of four short videos:

•The first video is a montage of video footage recorded at Viacom New Media featuring the developers playing around during development (including running around outside during a thunderstorm), showing off a production baby, and ending on Butt-Head saying "Dumbass!" while the word is superimposed over a picture of a developer.

•The second video is another montage of videos and pictures recorded during development (including the team going swimming and posing on a couch with Beavis and Butt-Head statues) set to an original rock song written for guitar and sung by one of the developers. Hatman also makes appearances in this video.

•The third video is a montage of video footage recorded during the making of the game's beta, which according to the video was completed on August 25, 1995 at 4:45 in the morning. The video prominently features the developers excitedly screaming "Beta" over and over again, before showing them lying in the hallway of the studio exhausted and ending with the quote "These kids are intense...." on screen.

•The fourth video is a crudely-made CG animation of Hatman floating through space, and is believed to be the earliest instance of the easter egg made for a game.

At the Veterans Hall, select the Foot and and click the top-left, top-right, bottom-right, and bottom-left corners of the building's sign in that order. A sequence will play out where the stuffed grizzly bear from the Insane Wing appears in front of the building and Butt-Head tells Beavis to "check in his anal cavity". Beavis then reaches inside the bear's anus and pulls out a red piece used in the puzzle game Zoop, which was also published by Viacom New Media around the same time as this game, before putting it back inside claiming that he felt something, but couldn't grab it, and then cutting to the game's title screen. Presumably, this sequence was scrapped from being used in the Insane Wing, but left in the game by hiding it in a different location.