Master Quest is a second quest of OoT. Like how in the first Zelda game, when you put your name as ZELDA, everything is rearranged, but the game is basically the same? It's like that.
I ordered The Wind Waker from Amazon a few days ago, and OoT/Master Quest has already arrived at my house. However, I won't be at my house until friday since I'm at school, so I guess it sucks to be me.