The Substance versions are basically "extended" versions of the original game. For the MGS2 Substance version, VR missions were added, as well as a mode called Snake Tales, where you do some missions as Snake. MGS3's Subsistence version had a new camera for the original game, and included online play. There was also a bonus disc with Subsistence, which was basically an interview with Hideo Kojima (although I think you had to pre-order Subsistence back then to get it).