By connecting Rayman 3 (GBA) to Rayman 3 (GameCube), the player can unlock numerous short bonus levels in the GBA version for every 100 out of 1000 Lums the player has collected for a total of 10 bonus levels. A secret 11th bonus level 'Ly's Punch Challenge 3' is unlocked when the GBA version is connected to a fully completed game of Rayman 3 on the GameCube with the 2D Nightmare minigame unlocked and played through as well.

In the original console releases and PC version of the game, the fourth section of the first world The Fairy Council has a fairy say in a cutscene, "Oh my god, what is going on here?" Then later, "Oh my god, its an unspeakable atrocity!" The phrase 'Oh my god' was removed in the HD remaster for PlayStation 3 & Xbox 360. Oddly enough, in the HD remaster, the minigame Crush maintains the phrase as a reactionary on-screen quote if players manage to score 10 consecutive hit combos.

2D Nightmare is a extra minigame exclusively featured in the Nintendo GameCube version of the game. Its aesthetics are based on 'Picture City' from the original Rayman, and its intended unlock method is by connecting both the GameCube & Game Boy Advance version of Rayman 3, with the latter version requiring that all levels are completed. However, due to a programming error in the GBA version, the final boss level of the game 'Heart of the Ancients' is never counted as complete due to the game not saving after the credits roll. It was assumed hacking via Action Replay codes was the only way to play 2D Madness. However, 20 years after both games released, it was discovered that the GBA version contains hidden in-game cheat codes.

On the game's world map screen, holding the Select button while inputting:
• R/A/A/A Unlocks All Powers
• B/B/B/A/A/A Gives 99 Lives
• UP/LEFT/DOWN/RIGHT/B/A/L/R Completes All Levels
• DOWN/UP/DOWN/UP/A/LEFT/B/RIGHT 100% Complete of Levels, Powers, Lums, Cages & 99 Lives

The last two cheat codes mark every level in the game as complete, including the final boss level. Entering either code will allow 2D Nightmare to be unlocked officially in the GameCube version without any hacks to access.

In 2021, a secret display mode for the PlayStation 2 version of the game was discovered that involves first setting the standard video output to 480p (through the "Progressive Scan Mode" option), and then starting a new game with the profile name "PSONE". Doing this will cause the game to lower the standard output from 480p to 240p and disable texture filtering, making it more closely resemble a PlayStation game. For unknown reasons, this mode is referred to as "Christian Slater mode" in the source code.

Various characters from Rayman 2: The Great Escape make a Hidden Appearance:
• Hidden in an alcove in The Hoodlums Headquarters, Razorbeard and his Pirates can be seen in a pose reminiscent of The Last Supper by Leonardo da Vinci.
• A statue of Ly the Fairy appears in a Secret Room found in The Longest Shortcut.
• Sssssam the Snake makes a cameo as a statue in Razolf's Castle in The Bog of Murk.

During the first level of the game, while in the Fairy Council, there is a reference to The Legend of Zelda when Andre encounters a fairy.

Billy West, voice actor for Murfy, previously voiced Rayman in the animated Rayman series.

Within the game's data is an unused music track called "Ice Dance". This is from the film Edward Scissorhands.

Before the final boss fight, the player can find a secret room containing four green jewels and three animals in cages: the Xowar, a blue Mawpaw and a Glute. In order to get to the room, the player must have accumulated a total score of 43,001 throughout the level.

In the PlayStation 2 release, the music for the Bog of Murk sounds different from all other releases.

Murfy's last quote in Rayman 3: Hoodlum Havoc is "See you in Rayman 4", so it is probable that he was to appear in the cancelled Rayman 4. Or he may have been referring to Rayman 3's sequel, Hoodlum's Revenge, where he appeared.

Near the beginning of the first Teensie Highway, where huge letters spell the word love, the USS Enterprise from Star Trek can be seen. The Enterprise was probably placed here because the Teensie Highway is a wormhole, and wormholes are encountered frequently by the Enterprise.