The difference is mostly bug fixes or minor detail changes. In No Mercy I believe v1.1 fixes a save bug that was in v1.0. I had to send my copy back to THQ because of that. Another example is in Zelda Ocarina of Time where Ganondorf acutually coughs up blood (v1.0) which is changed to green stuff in the other two versions (1.1,1.2). Those kinds of things are usually the reason for the different versions.