In the Japanese version of the game, inputting your name as とたけけ (Totakeke) change the file select screen's music into a remix of Totaka's song.

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.

The character Richard in Link's Awakening actually began as a non-Zelda character in a game called "Kaeru no Tame ni Kane wa Naru" which translates into "For the Frog the Bell Tolls". This game was the starting point for the Link's Awakening game engine.

When you visit Richard's villa, if you wait for around two and a half minutes and listen to the music, you'll be treated to an instance of the elusive 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, and Luigi's Mansion, and most famously, Animal Crossing.

You can return a hook to a fisherman in exchange for a necklace. You can then return the necklace to a mermaid in exchange for a scale from her tail. 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, the Hippo from the Animal Village had what appear to be breasts. This was changed during its localization to remove the breasts and any suggestion of clothing to cover up its naked body.

In the German version, after a Buzz Blob turns into a Cukeman, they will say:
"Nie Ohne Kondom!"
translated to "Not without a condom!"
and also "Gib Mir Deinen Saft, Ich Geb'Dir Meinen"
translated to "Give me your juice, I'll give you mine."

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 makes their character name "ZELDA" they are treated to a salsa remix of the game's main theme. This could also be a nod to the original Zelda on the NES, where entering the name "Zelda" on the second save slot results in the game starting on the second question immediately.
(Note: "ZELDA" must be in all capitals.)

Documents about Link's Awakening in the Hyrule Historia show an image with two characters fighting an enemy and a note next to it that reads "What're we gonna do about 1P mode?" suggesting the game was originally multiplayer.

If you steal from the shop keeper, the game will forever brand you as "THIEF" and the shop keeper will kill you upon re-entering for the first time. However, the games's photographer will snap a picture of you in the act, making this a required event if you intend to complete the photo album.

Link's Awakening features a large number of cameo appearances from various Nintendo characters.