The English manual and prologue for Star Fox Adventures implies a bigger backstory for Krystal, in that she's the sole remaining survivor of her doomed home planet, "Cerinia", and that she's been roaming the galaxy in search of answers for the truth of her family's death, until she receives a distress call from Dinosaur Planet. With how the manual states that Krystal "may finally be drawing closer to the truth" behind her parents' and planet's destruction, it seems Rare was loosely implying that Andross, who turns out to be the real villain of Star Fox Adventures and thus the culprit behind Dinosaur Planet's woes, was responsible for Cerinia's destruction. Krystal even says "It's you!" right before Andross imprisons her in the crystal at the top of Krazoa Palace.
However, it would seem the Japanese localization for Star Fox Adventures would completely eschew this backstory, removing all mention of Cerinia and as well as Krystal's dead parents. The Japanese prologue was even heavily simplified to this:
"Her name is Krystal. Guided by an SOS that she sensed telepathically, she came to this "Dinosaur Planet"..."
The Japanese website even states that "it is not known what her purpose is", which flies directly in the face of Rare's original story for her, that explicitly states that she was searching for the truth of Cerinia's destruction. To add more insult to injury, there isn't even any Japanese subtitle presented when Krystal gets knocked into the crystal by Andross in Krazoa Palace.
Curiously, the Japanese localization of Star Fox Adventures also heavily emphasizes Krystal having telepathic abilities, much more so than in the English version. This is noteworthy because neither Star Fox Assault or Star Fox Command, the next two story follows up to Star Fox Adventures that were developed and written in Japan, made any sort of mention of Cerinia. Star Fox Assault however would hugely emphasize her telepathic abilities, and its manual even describe Krystal the same way the Japanese version of Star Fox Adventures does, just as "a mysterious telepathic woman". This also applies to her trophies in Super Smash Bros. Brawl and Super Smash Bros. for Nintendo 3DS and Wii U that once again make no reference to Cerinia. It's very clear that the developers and writers behind Assault, Command and Smash Bros. in Japan were using the Japanese version of Star Fox Adventures as a reference, as opposed to the English version.
All in all, it would seem Nintendo of Japan had their own differing vision of what Krystal's character was from Rare, that being mostly just as a telepathic woman with a mysterious background, as opposed to Rare's original backstory of her being the lone survivor of her kind.
World 7 of Super Mario Bros. 2 (and in turn the original Doki-Doki Panic) only has 2 stages instead of the standard 3 used for stages in the rest of the game. This is due to the plotline in the manual of the original Doki-Doki Panic, where the final page of the book the twins were teleported into was torn out. This detail was not given an equivalent in Super Mario Bros. 2's plotline, and even in the original Japanese release was not mentioned in-game, and as such could come off as an oddity to players of the original version too should they not read the manual.
The English manual for Star Fox infamously states that the Lylat System is located "near the center of the Milky Way galaxy". However, this appears to be a localization quirk on Nintendo of America's part, as the original Japanese manual states that Lylat is located simply "near the center of a vast galaxy".
One of the enemies that appear on the Zoness stage, according to the official Japanese Star Fox 64 guidebook, is known as オブネマ (Obunema), or Obnema, a giant anthropod that can only be defeated with charge shots.
The Star Fox 64 Official Player's Guide renames it as "Kani" and claims that prior to Zoness' devastation, it was a favored delicacy in Zoness restaurants.
The Star Fox 64 Official Player's Guide gives Aquas' boss Bacoon a very different backstory from the official Japanese guidebook. The latter says that Bacoon is simply just a bioweapon made by Andross, but the former gives it a more elaborate background, claiming that it was an ancient monster that was jealous of the ancient civilization and their temples/islands above the ocean's surface, and overtime it learned how to control the other aquatic lifeforms within Aquas' oceans, such as the explosive Starfish, which were then commanded by Bacoon to migrate to the ice cap and detonate, resulting in the polar cap being melted and all of the islands submerged into the sea forever, essentially explaining the ancient undersea ruins throughout the Aquas stage.
The section for passwords in the manual for Wario Blast shows an image of the game's title screen with a debug code (2264) that lets the player start the game with all power-ups as Wario. It is unknown if this was an oversight, or intentionally included.
The game's instruction manual features an extensive backstory for Gex, who lived in Maui with his mother and siblings, whilst his father was working at NASA. Due to an incident involving a band-aid floating in a fuel tank, Gex's father was killed, causing Gex to become a shut-in, sitting and watching TV all day.
After moving to California and his mother selling the TV away, Gex runs away from home and sleeps in the garage of a local punk he befriends. At his deteriorated state, Gex imagines an invisible friend known as "The Mayor." With another death in the family, this time being Gex's Uncle Charlie who was the original model for the Izod shirt logo, this leaves Gex's family with an inherited fortune of 20 billion dollars.
With his share of the money, Gex leaves his family behind, returns to Maui, and purchases a mansion with the largest TV set in the world and enough food to last him for decades, so that he'll never have to leave the television again.
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On page 6 of the game's manual, there's a news article about how a protest group called A.R.S.E. (American Road Safety for Everyone) is pushing to get motorcycles banned from Liberty City, and might also be responsible for getting bicycles banned from Liberty City a few years prior. This explains the absence of bicycles and motorcycles in Grand Theft Auto III.
In the game's opening cutscene after Dr. Yoshiyama digitizes himself, several blocks of what seems to be gibberish appear on-screen before the computer corrupts. This gibberish is actually a secret message written in Japanese romaji and then coded through a cipher where all vowels are omitted from the text, except for when a word starts with a vowel. Decoding the message reveals what seems to be the last conversation Yoshiyama had with the C-Life woman featured in the cutscene, the mother of Pulseman, suggesting that he gave up his human life ("Do you realize what you've done? You'll never be human again now.") out of love for his creation and resulting in the conception of Pulseman. A cosmetic detail hinting at the nature of the undeciphered message being a conversation are differences in the speed at which each text box appears typed out on-screen (i.e. a slight slowdown during "I'm just a heartless program"). However, not only does this affair reveal the origin of the game's hero, it also has implications about the origin of the game's villain.
Dr. Yoshiyama's whereabouts during the events of Pulseman are never stated, but through information provided in the game's manual, it is suggested that he was corrupted during his time in cyberspace and transformed into the game's antagonist Dr. Waruyama. This theory is supported by the manual listing Yoshiyama's entry into cyberspace during the cutscene and Waruyama's birthdate, December 31, 1999, as occurring in the same year. However, Waruyama appears to be a full-grown adult by 2015 when the main events of the game take place despite technically being 16 years old and less than two years older than Pulseman.
This age discrepancy suggests that Waruyama would have to be at least a half C-Life or full C-Life himself in order for him to originally have been "born" as an adult (given that C-Lifes are computer-generated life-forms), and in this case, for him to originally have been the adult Yoshiyama. Since Yoshiyama was implied to have transformed into at least a half C-Life following the deciphered conversation, this suggests that Waruyama's "birthdate" actually refers to the exact date when Yoshiyama was transformed into Waruyama in the first place.
Additionally, there are similarities between the two names, with "Waruyama" being similar to "Bad mountain" ("悪い山" or "Warui yama"), and "Yoshiyama" appearing similar to "Pleasant mountain" ("楽しい山" or "Tanoshī yama").
The English description for the game's 2009 re-release on the Wii Virtual Console states outright that Yoshiyama did transform into Waruyama, although there are no known Japanese sources that also confirm this.
Raoh and Heart are the only characters in the game who cannot crouch and subsequently cannot block low. The game's manual explains that the reason why Raoh does not crouch is because "it's not like a king to kneel."
The Japanese and PAL region releases of Spirit Camera: The Cursed Memoir have exclusive bonus content that can be accessed after completing Story Mode by scanning an augmented reality marker on the back of the instruction manual to the Wii port of Fatal Frame II: Crimson Butterfly, released only in Japan and PAL regions under the name Project Zero 2: Wii Edition. Scanning the marker will unlock models of Mio and Mayu Amakura as they appear in that game to view in Spirit Photography mode. Because the Wii port of Project Zero 2 was never released in North America, these models were made inaccessible in the North American release of Spirit Camera: The Cursed Memoir.
In the game's North American manual under the "Even More Sonic Super Play Tips" section, the last tip subtly addresses how to deal with glitches resulting from running too fast by branding them as "diabolical traps" set by Dr. Robotnik that "take advantage of Sonic's ultra-fast speed".
The developers had help from former NYPD officers Bill Clark and Tom Walker to make the game more accurate. Despite this, the game was seen as disrespectful by the rest of the NYPD and was boycotted. This has lead to the firing of both officers involved with the game, changing the in-game police from the real live NYPD to the PDNY, and including a piece of paper with each copy stating that the NYPD does not endorse the game.
On page 10 of the instruction manual is a segment demonstrating how to create a character. The screenshot accompanying this section shows a character being named "Homestar", referencing Homestar Runner, a popular online Flash series.
In the official strategy guide for EarthBound, there are pages about the town's attractions, accompanied by fun facts, such as: • Onett Has a population of 3,500 people and 2 dogs. • Twoson has 10 vendors in the park and 15 mushrooms. • In Threed, there are 2 Graveyards, 2,000 zombies, and a grand total of 0 lions, tigers, and bears. • In Dusty Dunes Desert, there are 2,000,001 Cacti, and 5 people living there. • There is an average of 0 Temper Tantrums in Dalaam. • Deep Darkness has 4,000,603 Mosquitos.
EarthBound's Official Strategy Guide contains pictures of real locations. This may be to give the guide a more realistic feel, as if it wasn't a guide. The strategy guide also includes newspaper articles, which mainly revolve around Ness and his party's journey.
The English manual and prologue for Star Fox Adventures implies a bigger backstory for Krystal, in that she's the sole remaining survivor of her doomed home planet, "Cerinia", and that she's been roaming the galaxy in search of answers for the truth of her family's death, until she receives a distress call from Dinosaur Planet. With how the manual states that Krystal "may finally be drawing closer to the truth" behind her parents' and planet's destruction, it seems Rare was loosely implying that Andross, who turns out to be the real villain of Star Fox Adventures and thus the culprit behind Dinosaur Planet's woes, was responsible for Cerinia's destruction. Krystal even says "It's you!" right before Andross imprisons her in the crystal at the top of Krazoa Palace.
The English manual for Star Fox infamously states that the Lylat System is located "near the center of the Milky Way galaxy". However, this appears to be a localization quirk on Nintendo of America's part, as the original Japanese manual states that Lylat is located simply "near the center of a vast galaxy".
One of the enemies that appear on the Zoness stage, according to the official Japanese Star Fox 64 guidebook, is known as オブネマ (Obunema), or Obnema, a giant anthropod that can only be defeated with charge shots.
The Star Fox 64 Official Player's Guide gives Aquas' boss Bacoon a very different backstory from the official Japanese guidebook. The latter says that Bacoon is simply just a bioweapon made by Andross, but the former gives it a more elaborate background, claiming that it was an ancient monster that was jealous of the ancient civilization and their temples/islands above the ocean's surface, and overtime it learned how to control the other aquatic lifeforms within Aquas' oceans, such as the explosive Starfish, which were then commanded by Bacoon to migrate to the ice cap and detonate, resulting in the polar cap being melted and all of the islands submerged into the sea forever, essentially explaining the ancient undersea ruins throughout the Aquas stage.
The section for passwords in the manual for Wario Blast shows an image of the game's title screen with a debug code (2264) that lets the player start the game with all power-ups as Wario. It is unknown if this was an oversight, or intentionally included.
The game's instruction manual features an extensive backstory for Gex, who lived in Maui with his mother and siblings, whilst his father was working at NASA. Due to an incident involving a band-aid floating in a fuel tank, Gex's father was killed, causing Gex to become a shut-in, sitting and watching TV all day. 
The game's User Guide shows that the options menu at some point in development displayed the Quit Button instead of the Demos and Credits button.
In the game's opening cutscene after Dr. Yoshiyama digitizes himself, several blocks of what seems to be gibberish appear on-screen before the computer corrupts. This gibberish is actually a secret message written in Japanese romaji and then coded through a cipher where all vowels are omitted from the text, except for when a word starts with a vowel. Decoding the message reveals what seems to be the last conversation Yoshiyama had with the C-Life woman featured in the cutscene, the mother of Pulseman, suggesting that he gave up his human life ("Do you realize what you've done? You'll never be human again now.") out of love for his creation and resulting in the conception of Pulseman. A cosmetic detail hinting at the nature of the undeciphered message being a conversation are differences in the speed at which each text box appears typed out on-screen (i.e. a slight slowdown during "I'm just a heartless program"). However, not only does this affair reveal the origin of the game's hero, it also has implications about the origin of the game's villain.
The Japanese and PAL region releases of Spirit Camera: The Cursed Memoir have exclusive bonus content that can be accessed after completing Story Mode by scanning an augmented reality marker on the back of the instruction manual to the Wii port of Fatal Frame II: Crimson Butterfly, released only in Japan and PAL regions under the name Project Zero 2: Wii Edition. Scanning the marker will unlock models of Mio and Mayu Amakura as they appear in that game to view in Spirit Photography mode. Because the Wii port of Project Zero 2 was never released in North America, these models were made inaccessible in the North American release of Spirit Camera: The Cursed Memoir.
In the game's North American manual under the "Even More Sonic Super Play Tips" section, the last tip subtly addresses how to deal with glitches resulting from running too fast by branding them as "diabolical traps" set by Dr. Robotnik that "take advantage of Sonic's ultra-fast speed".
The developers had help from former NYPD officers Bill Clark and Tom Walker to make the game more accurate. Despite this, the game was seen as disrespectful by the rest of the NYPD and was boycotted. This has lead to the firing of both officers involved with the game, changing the in-game police from the real live NYPD to the PDNY, and including a piece of paper with each copy stating that the NYPD does not endorse the game.
On page 10 of the instruction manual is a segment demonstrating how to create a character. The screenshot accompanying this section shows a character being named "Homestar", referencing Homestar Runner, a popular online Flash series.
EarthBound's Official Strategy Guide contains pictures of real locations. This may be to give the guide a more realistic feel, as if it wasn't a guide. The strategy guide also includes newspaper articles, which mainly revolve around Ness and his party's journey.