Between the original and the master quest?
I went into game stop the other day to ask about a midnight launch for saints row 2... Her exact words were "wats a midnight launch?"
Busagi Nephry: I am a teenager; I must roll my eyes at someone twenty years older than I am at least once in my life.
People say that playing video games makes you have no life. Yet here I stand.
That guide just has changes between various versions of OoT - 1.0, 1.1, 1.2, and the Gamecube version, not about the differences between OoT and MQ. There isn't a guide specifically about those differneces.
Fortunately, the only differences between OoT and MQ are the dungeons. They have the same layout, but the monsters, puzzles, and items are all in different places, and they usually have to be done in a different room order. Some dungeons are easier (especially, most say, the Water Temple, which is done "backwards" compared to the OoT version), but most are somewhat harder.
Other than that, there's nothing different at all. The dungeons are all in the same place on the Overworld, and you have to solve the same puzzles to open them.