In the Astral Observatory, there is a picture of a dolphin hidden under a small pot. It's thought to be a reference to Dolphin, the Gamecube's code name at the time.
The enemy character Red Bones' name in Japanese is "Buraddi Honenoko", which translates to "Bloody Son of Bone" (or "Bloody Dull Bones"), which could hint to a Koopa Troopa having met a gory demise, then being resurrected as a Dry Bones, but still had a stained shell.
There's an item hidden in the game's code called the "Water Boots." They have no effect, but putting them on uses the same animation and sound as the Iron Boots. It's speculated that they may have been used for underwater swimming, or sinking underwater like the Iron Boots from Ocarina of Time.
A popular long-standing fan theory about Super Mario Bros. 3 was that it was actually an elaborate stage play.
The commonly cited evidence that supports this theory include: •The game's title screen starts with the rise of curtains, and the game ends with the fall of curtains, as well as curtain calls for each World and several characters during the end credits •Some platforms are hanging down from the "sky" by wires implying it's scenery being hung from the ceiling •Some platforms are bolted to the wall and cast shadows against the "sky" suggesting it's a backdrop •If Mario/Luigi kneels on white block platforms for six seconds, he will fall behind them and can walk behind the scenery •Some platforms are sticking out through carved-out slots in the backdrop suggesting they are being controlled by hidden machines behind the set •Each regular stage ends by exiting stage left and going "backstage" into the dark goal area •Every injury or death in a stage is Mario/Luigi messing up the scene (the "Mario was never once in any real danger" part in the attached image is not necessarily true as unintended injuries and deaths can happen in theatre)
One overlooked piece of circumstantial evidence that supports this theory concerns the fact that the Kings of each World that are transformed into different creatures by the Koopalings are never actually seen being transformed into creatures, or transforming back into humans after Mario defeats a Koopaling. The way every Koopaling defeat plays out shows Mario falling from the airship holding the King's magic wand, the scene fades to black, and then the lights come back up inside the castle showing the King already transformed back into a human before either the wand or Mario return to the castle. This suggests that the Kings were never transformed in the first place, because they were all actors waiting to get into place for their scenes, and the transformations are the suspension of disbelief. It should be noted that the Game Boy Advance version of the game partially discredits this by adding cutscenes showing each King being turned into creatures by the Koopalings, but they are still are not seen being transformed back into humans.
In a Q&A interview to promote the release of Super Mario Maker in 2015, Shigeru Miyamoto confirmed the theory, that the game was all a performance.
There is a hidden "Red Man" in the Corel Prison. The model is hidden from view in normal gameplay. There are no other models like this in the game, and it is thought to be a signature from one of the designers.
All of the Star Fox pilots have robotic legs. It is theorized that they had their legs amputated to prevent blood from rushing down to them in the high G-forces they would experience, causing them to pass out. Modern day pilots wear tight fitting clothing around their legs for the same reason.
Various screen-shots you take in the game have a secret watermark that contains data for your account ID, the time the screenshot was taken, and the IP and data of the server you were playing on. It's speculated that this was mainly used to identify and punish internal leaking of images during development.
Playing Ashley's music on the record turntable fast enough will speak the words "I have granted kids to hell!" However, in Nintendo Power issue 193, Nintendo stated that it was an accident, and the words come out like that due to the turntable skipping over parts of the song, and only playing certain pieces of the track.
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When Link sprinkles Magic Powder or uses a Mystery Seed on a Buzz Blob, it will transform into an enemy called a Cukeman who Link can talk to and hear several short phrases. Each localization of the game features completely unique Cukemen phrases, often making vague references to real-life people or things.
In the Japanese release, the Cukeman's dialogue string is a series of catchphrases that ends with "…That concludes this collection of R-Moto-isms. It has absolutely nothing to do with the game!" "R-Moto" is most likely a nickname for the game's character designer Masanao Arimoto, suggesting that the Cukeman's dialogue originally consisted of phrases he commonly used during development.
In the English release, this dialogue is changed, causing the Cukeman to say nonsensical phrases like the stereotypical Jamaican greeting "Hey Mon!", as well as "It can display millions of polygons!" immediately followed by "I definitely need it, as soon as possible!". These last two lines are most likely a reference to the Nintendo 64 which was in early development stages at the time of the game's release.
In the original German release, the Cukemen will say more suggestive or vulgar phrases courtesy of Nintendo of Europe localization translator Claude Moyse. Two of the phrases include "Gib Mir Deinen Saft, Ich Geb'Dir Meinen" which translated from German to English means "Give me your juice, I'll give you mine.", as well as "Nie Ohne Kondom!" which translates to "Not without a condom!" The "Gib Mir Deinen Saft, Ich Geb'Dir Meinen" line is most likely a direct reference to the 1992 song "Saft" by German hip-hop group Die Fantastischen Vier, of which that line is its hook, and peaked at #19 on the German singles chart the year prior to Link's Awakening's release. Because the song openly promotes the sexual exchange of bodily fluids, the "Nie Ohne Kondom!" line was presumably added by Moyse to jokingly riff off it while promoting safe sex to older players. The Link's Awakening DX release in Germany removed these references and phrases and instead changed them to in-game hints.
In the French release, the dialogue is changed once again to more nonsensical phrases before ending the dialogue string with "Lots of kisses from Kyoto! VERO". This last line features the name "VERO" and a unique heart sprite tacked on at the end as a signature, most likely from the localizer of this dialogue.
In the Hyrule Historia, it is revealed that there are three timelines sprouting off of Ocarina of Time. It's revealed near the start of Ocarina of Time that the great Deku tree dies, leaving a sprout to grow and one day replace him. The original Legend of Zelda takes place in the timeline in which Link is defeated in Ocarina of Time, and the first dungeon takes place inside a tree in a secluded area, likely to be the remains of the Great Deku Tree. In the timeline of Ganon being defeated and Adult Link remained, the Deku Sprout grew into a new Great Deku Tree which we see in Wind Waker. It makes sense that Ganon would have destroyed the sprout once he gains control of the land.
During day 3 at the Romani Ranch, you can trigger a conversation where Romani tells you that that night is finally the night when she gets to drink Chateau Romani. According to the sisters, the properties of Chateau Romani are so potent that children aren't allowed to drink it under normal circumstances, drawing parallels with alcohol in the real world. It's also only served in the Milk Bar, where children aren't allowed, and is only open at night. The scene at the ranch unfolds with Cremia stating that she acknowledges Romani's adulthood, and asks her little sister to sleep in her bed tonight. Cremia dishearteningly utters "See you... Tomorrow... OK?" while Romani cheerfully adds "See you tomorrow!"
It seems as though Cremia knows that they're about to die, and is giving Romani the drink to dull her senses, so that she remains blissfully unaware of their destruction.
At the beginning of the game, you come across a warped dead Deku like figure. We can presume that this Deku scrub died in a horrible way. Additionally, later in the game, the Deku butler directly states that Link reminds him of his son, and he is seen weeping over the figure in the end credits. It's likely that this figure is the butler's son, and his spirit has been with you throughout the whole game.
At the very end of the game's ROM is a secret message from the game's director, Axel Brown;
Dear Hacker, yes there are some cheats and other hidden stuff in Metal Morph. Some are on the title page and some are not!! All standard cheats are possible, you're just gonna have to find them, b-u-u-u-d-d-d-d-y-y-y-y-y!!! ---- axel@origin.ea.com
The spelling of "buddy" in this message may be hinting at a potential cheat code in the form of B, Up, Up, Up, Down, Down, Down, Down, Y, Y, Y, Y, Y, although the effects of the code and how to activate it (if it exists at all) have yet to be discovered.
It's speculated that the forest and water temples in Ocarina of Time were originally wind and ice temples. The symbol on the Water Medallion from the Water Temple appears to have a snowflake on it, and the Forest Medallion design resembles a fan. This connection is further supported by the interior of Ganon's Tower, which is based on different temples. The Forest Temple portion of the tower has a wind puzzle based around fans, and the Water Temple portion of the tower is based on ice.
There's evidence suggesting that the psychic type in Pokemon is weak to bug, ghost, and dark types because they are basic fears, and fear can manipulate the mind. This is further implied by the ability "Rattled" (or "Jitter" in Japanese) where the user's speed stat is raised one stage when hit by bug, dark, or ghost-type moves, implying they have been shook up, or scared.
The 7th dungeon of Twilight Princess, "City in the Sky", is speculated to be based on a painting called "Another World" by M.C. Escher. The creatures, seen on the walls in the painting resemble the Oocca from the game. In the Twilight Princess dungeon, the Oocca are found running on the walls and floor.
There's an old Japanese idiom that says, "A duck comes along carrying a leek". It means a happy convenience, as duck with leek is a popular meal. The Pokemon Farfetch'd is based on this saying. The anime also states they are rare due to them being delicious. It seems that Farfetch'd were designed to be eaten from the very beginning. Any notion of them being used as food was later toned down or dropped. Along with the word "leek", which is now called a stick or a stalk.
The Gyroids bear a strong resemblance to Haniwa; clay figures made for ritual use and buried with the dead. This explains why Gyroids can only be obtained by digging, and also implies that you have just dug up someone's grave. This likeness is referenced in the Japanese version of Animal Crossing: City Folk, where the auction house owner Lloid is named "Haniwa-Kun".
In the Astral Observatory, there is a picture of a dolphin hidden under a small pot. It's thought to be a reference to Dolphin, the Gamecube's code name at the time.
The enemy character Red Bones' name in Japanese is "Buraddi Honenoko", which translates to "Bloody Son of Bone" (or "Bloody Dull Bones"), which could hint to a Koopa Troopa having met a gory demise, then being resurrected as a Dry Bones, but still had a stained shell.
A popular long-standing fan theory about Super Mario Bros. 3 was that it was actually an elaborate stage play.
There is a hidden "Red Man" in the Corel Prison. The model is hidden from view in normal gameplay. There are no other models like this in the game, and it is thought to be a signature from one of the designers.
In the console's BIOS, there is a unused disk graphic which represents a DVD Video. It's possible that there were plans for support of DVD Videos.
In Super Street Fighter II: The New Challengers, there is an unused graphic in the game with the name "Sarah". This may have been Cammy's early name.
All of the Star Fox pilots have robotic legs. It is theorized that they had their legs amputated to prevent blood from rushing down to them in the high G-forces they would experience, causing them to pass out. Modern day pilots wear tight fitting clothing around their legs for the same reason.
It's speculated that the forest and water temples in Ocarina of Time were originally wind and ice temples. The symbol on the Water Medallion from the Water Temple appears to have a snowflake on it, and the Forest Medallion design resembles a fan. This connection is further supported by the interior of Ganon's Tower, which is based on different temples. The Forest Temple portion of the tower has a wind puzzle based around fans, and the Water Temple portion of the tower is based on ice.
The 7th dungeon of Twilight Princess, "City in the Sky", is speculated to be based on a painting called "Another World" by M.C. Escher. The creatures, seen on the walls in the painting resemble the Oocca from the game. In the Twilight Princess dungeon, the Oocca are found running on the walls and floor.