In an Iwata Asks interview conducted to promote the release of The Legend of Zelda: Spirit Tracks, Takashi Tezuka revealed that the world of Link's Awakening was strongly inspired by the 1990 TV series Twin Peaks. According to Tezuka, he was fascinated by how the show was able to mine drama out of a small cast of "suspicious types" confined to a single town and sought to replicate that approach with Link's Awakening, stating that "while it would be small enough in scope to easily understand, it would have deep and distinctive characteristics."

There is unused text in the game's ROM that says "You've got a Shovel! Now you can feel the joy of digging!" Additionally there is unused chest data in one of the caves for a shovel suggesting that the shovel was originally meant to be obtained from a chest rather than being purchased.

The first idea for the game was a port of A Link to the Past, but it eventually evolved into an original game.

If the player has the bow and the bomb equipped, and presses both the bow and bomb buttons at the same time, Link will shoot the arrow with a bomb attached. Bomb arrows in this game are thought by some to be a glitch; however, this has never been confirmed nor denied by the developers.

When Link hits a Cucco, Marin scolds him, but if Link hits a Cucco too many times, Marin will temporarily change her attitude and encourage Link to keep attacking it. These are traits of a Psychopath.

If Link plays the "Ballad of the Wind Fish" while in the presence of Marin, she will say, "Not very good... Eh? What? Did I say something? No, you're hearing things..."

In the German version of the game, entering Link's name as "MOYSE" will change the background music to a techno remix. The code refers to the famous German translator Claude Moyse. In the DX version of the game, the code will change the music to a remix of Totaka's Song.

Richard in The Legend of Zelda: Link's Awakening is likely based on the main character for the game Kaeru no Tame ni Kane wa Naru (or "The Frog for Whom the Bell Tolls"). This is evident in his villa, in which the music that is played is a remixed version of the main theme from that game, and the frogs found hopping around his villa being a reference to the gameplay of his own game. Link's Awakening also uses the same engine as For the Frog the Bell Tolls.

There is a variant of Totaka's Song found in the game's coding. It is still unknown if the song is played anywhere in the actual game.

In the Japanese version of the original game, inputting your name as とたけけ (Totakeke) will change the file select screen's music to a remix of Totaka's song. This would be implemented in all versions of the game's remake.

In the middle of the game, you have a conversation with Marin. She says that her dream is to fly away from the island. At the end of the game (Spoiler:after you wake up the Wind Fish and the island disappears), if you haven't lost any lives, you can see either Marin's sprite with wings (original) or a portrait of Marin that dissolves to reveal a seagull behind it (DX Remake). This hints that Marin was able to escape the island and got her wish to fly away.

Mr. Write is likely based on an advisor in the original SimCity, who had a nearly-identical appearance and name, Dr. Wright. The theme that plays in Mr. Write's house is also from the SNES version of SimCity, where it serves as Dr. Wright's theme.

There is an enemy called "Anti-Kirby." It has the ability to inhale almost anything. Anti-Kirby is based on the character Kirby, from the Kirby series.

Before destroying the support pillars and causing the fourth floor to collapse onto the third, the four rooms in the center of Eagle's Tower's third floor are entirely different, consisting primarily of an extremely large pit. Of these rooms, the upper two are inaccessible and never normally seen in-game. It appears the one on the left was meant to be used, but due to the way the crystal switches work, the blocks controlled by them will always deny you entry. And even if it was accessible, the pit is too open and can easily lead to getting trapped on the second floor. Interestingly, while the room is inaccessible, it was still updated after the first version.

To the right of that room is one that was definitely never intended to be used at all, consisting only of a "down" staircase leading up to the fourth floor, presumably for testing purposes. It's also the only way to get up there. (Leaving the 4F area in any direction will take you to blank "default" rooms.)

These rooms are also present in the DX version.

When the player is inside Richard's villa, waiting around for two and a half minutes will trigger an instance of the famous Totaka's Song.

Totaka's Song is a small ditty that composer Kazumi Totaka likes to hide in many of works, including Mario Paint, Yoshi's Story, Luigi's Mansion, and most famously, the Animal Crossing series.

Part of the trading sidequest involves returning a fishook to a fisherman in exchange for a mermaid's necklace. The player then returns the necklace to the mermaid who gives Link a scale from her tail in return. In the Japanese and some European versions of the game however, Link receives a pink bra instead of a necklace. This explains the mermaid's shy and anxious behavior around Link. The pink bra, most likely deemed inappropriate, was changed to the necklace in the American version and later European versions of the game.

In the original Japanese version of the original game, the Hippo Model from the Animal Village had what appear to be breasts. This was changed during its international localization to remove the breasts and any suggestion of clothing to cover up its naked body. In the game's remake, the Hippo Model retains her hourglass figure, but is now fully clothed to maintain a satisfactory parity for all regional releases of the remake.

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 issues 44 and 48 of Nintendo Power, there are a number of early screenshots from a pre-release copy of Link's Awakening.
These show that the Wind Marimba was originally a pair of cymbals, you could carry more than one of Crazy Tracy's medicine, and you could also carry the Guardian's Acorn. There also appears to be another item that wasn't in the final game that looks like a stone fragment. This was also a prize available in the crane mini-game.

There is also an early version of the world map that is completely different from the final game. It appears to be a highly condensed version of Hyrule from A Link to the Past map. This was likely used as a placeholder during development.
It also seems that the boss battle with Moldorm would have taken place in a room that is completely different from the final version of the game.

If the player names their character "ZELDA" in all capital letters ("LOLO" in the French release; "ぜるだ" in the Japanese release) they are treated to a salsa remix of the game's main theme. This could also be a nod to the original The Legend of Zelda on the NES, where entering the name "ZELDA" on the second save slot results in the game starting on the second quest immediately.