master quest is harder and the dungeon layouts are different. (possibly reversed). Other than that, they're the same game.
im not sure exactly, I suppose the puzzles are more difficult and the enemies take more hits to defeat.
As someone who owns the game and has played through it, I'll answer... The only difference between OoT and MQ are the dungeons. Period. The dungeon layouts are the same, but the puzzles within are different. For instance, the Deku Tree and Dodongo's Cavern have Song of Time blocks that weren't in the original, which means you'll have to backtrack just before you become an adult. As a result of the dungeons being changed, the Golden Skulltula locations within the dungeons also changed. The enemies did not get harder, however. It's the same engine, the same stats on enemies, everything. The only major difference you'll notice is if you got a launch copy of Ocarina (1.0), since Master Quest is based off of Ocarina 1.2, which fixed a lot of the glitches that made the endgame fun (such as Swordless Link), changed the emblem on the Mirror Shield, and Ganondorf spits green blood instead of red. Think of it as the "Second Quest" of Ocarina.
