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In the Dam level, there is a blue metal trapdoor on the floor in a guardhouse that serves no purpose in the final game. Many believe it was part of an older objective that was taken out of the game. Some speculate that Bond previously had to retrieve his tracker bug for the mission in this hatch, since the message "Picked up a bug" can be found in the game's memory but is never used in the game. Others speculate Bond previously picked up explosives here for a lost objective requiring players to blow up the truck. Still others believe it was merely a quicker way to the comms room below the dam, since it is almost directly above it. It's true purpose remains a mystery.

On several explorable locations in the game, namely Altahe, Nepmos, Nodacrux, Rayingri, Eletania, Xawin and even Luna (Earth's moon,) strange sounds can be heard when the player exits the Mako and stands in a specific point of the map.

Although never confirmed by BioWare, the Mass Effect community has speculated that these peculiar noises are 'songs' from the insectoid and believed extinct race the Rachni.

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.

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.

Despite looking black-faced, Jynx wasn't meant to be racist. It is actually based off the Japanese Myth, Yama-Uba. Yama-Uba was described as having bright blond hair and a torn red kimono much similar to the design of Jynx.

The targets of the mission "Splinter Group" are four mutated raiders named Mick, Lee, Ralph, and Dan. This is a play off of the Teenage Mutant Ninja Turtles named Michelangelo, Leonardo, Raphael, and Donatello. The other similarities include their hideout being in the sewers, their name "Splinter Group" after the rat master "Splinter", their surfer-like language ("dude", "brah") and their craving for pizza used to lure them out.

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.

Shigesato Itoi first founded Ape Inc., the company that worked on EarthBound's predecessor Mother / EarthBound: Beginnings. Ape Inc. later reformed as Creatures Inc. with the help of Satoru Iwata. Ape Inc. worked on EarthBound, and later helped Game Freak develop the Pokémon series as the reformed Creatures Inc. Their influence can be seen in Pokémon. The main villain in Mother, Giygas, has a battle sprite that resembles Mewtwo. He also has a mental power called PSI. Additionally, there's an item in EarthBound called "Bag of Dragonite." There is also a Pokémon named Dragonite.

In Mother 2 (the Japanese version of Earthbound), the cultists of Happy Happyism appear with the letters HH on their forehead (for Happy Happyism). In Earthbound, a pom pom was added and the HH was removed, presumably to try to make the cultists look less like members of the Klu Klux Klan. Also, possibly because HH on an already Klan-like sprite could be construed to mean "Heil Hitler". The city "Threek" was renamed "Threed" in Earthbound. Like the cultists, this may also be to avoid any link to the Klan, as Threek could be seen as Three K's, or KKK.

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.

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.

It is widely considered that the lead hero is a reference to Marty McFly from the Back to the Future series. Both characters travel through time, use the term "heavy" and wear an orange life preserver. The lead hero also has a strong interest in movies, so this is possibly a development of that characteristic.