The Color Dungeon's music is a remix of the dungeon theme from the original The Legend of Zelda.

The Color Dungeon in the DX re-release is the only location in the game where green Rupees are found. These are worth five Rupees each, while blue Rupees, the only color found elsewhere (i.e. in all locations present in the original version of the game), are worth one. This is a reversal of the values of green and blue Rupees found in most other games in the series.

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.

One of the major additions to Link's Awakening DX is the photographer. On the screen where the photographer would be in the original version, there is simply an empty field with a single Moblin wandering around.

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.

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 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.