== READ BEFORE WATCHING ==
First things first, here's a list of every currently known difference in the GCN version:
The buttons were recolored (A is green, B is red, etc.)
Most things that reference the buttons were recolored too (but some things didn't change)
"Z" was changed to "L"
Zora Link has a different Zora Punch, see: • Japanese Majora's Mask: Zora Punch/Boomera...
Many text differences, see: • Majora's Mask: English Text Differences
Quite a few glitches were fixed; these same fixes can be found in the N64 PAL version. See: • European (PAL) Majora's Mask Play-Altering...
A good number of sound differences. See the description on the above-linked video.
Also, there are a few differences not caused by the ROM, but by the emulator on the Collector's Edition disc. I could not record these because I do not own an actual copy of GCN MM:
The game is very laggy in certain areas. See Siglemic's video of this here: • Video
Prone to crashing, and it crashes even more frequently when the rumble feature is turned on
There are some graphical issues, like in the Zora Healing CS; the Indigo-go members are standing behind Mikau the whole time! (Normally, they are introduced late in the scene, and they are revealed by a spotlight)
Just like the Gamecube version of Ocarina of Time, the US, Japanese, and European Gamecube versions of Majora's Mask are all identical except for text. This leads to a staggering number of changes in the Japanese version, because almost all of the Japanese differences have been completely erased.