Added/changed in Ocarina of Time Master Quest

The story stays the same, but there are obvious differences concerning the game and level design. Most of them are visible in the dungeons, which kept around the same "architecture", but the puzzles that we could find in every room changed a lot, having been remastered and often made more challenging. The progression of the player also changed (concerning the obtainment of key items in a different order). Also, the normal enemies (not including mini-bosses and bosses) also change in their numbers (more numerous) and locations. To my opinion, they were also a bit "smarter". There are even some new enemies which were not present in the original Ocarina of Time game, such as Like-Likes and cows in the belly of Jabu-Jabu).

Another modification concerned the Islamic symbols present in the original game. Instead of the originally present crescent moon on the Mirror Shield, we can see the symbol of the Spirit Temple in the Master Quest version. On the other hand, the music theme of the Fire Temple has also been modified, since the original one contained Islamic chants. This last modification had already been applied during the localization of Ocarina of Time for the European region. So this musical difference will not be obvious to you if you played an European version of the original game.

Sources:

• Personal experience and knowledge
• French Wikipedia article: http://fr.wikipedia.org/wiki/The_Legend_of_Zelda:_Ocarina_of_Time#Master_Quest