Some levels from the Game Boy Advance version were replaced with exclusive levels that feature vertical exploration in the N-GAGE version. There were also changes in the sound effects as well as the music in the N-GAGE version.

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.

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.