Alec may be able to elaborate on this better but here are a few version differences that should be noted:
-Text Speed: English vs. Japanese:
http://www.youtube.com/watch?v=atCLqVMsAxc-Morpha's Color
v1.1, v1.2
v1.0
-Stealing the Rod using hoverboots-Deku Stick on B and Saving: if you savewarp after stealing the rod, the sword that was equipped when you stole the rod gets deleted from your inventory. when you reload the save you will have stick on B.
if you savewarp AGAIN (with the MS missing from inventory):
on 1.1, 1.2, GCN, and VC - it automatically equips MS again
on 1.0 - you keep stick on B for as many savewarps as you want.
this is due to Nintendo fixing the oldest "Swordless Link" method where you savewarp out of the Ganon battle when Ganon knocks away your sword.
Also, what version of OoT is VC?