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I would have posted my response here, but alas, the 1000 character cap for visitor messages was too much for my wall of text (so I sent you a pm instead). In any case, to sum up my pm: 1) GPlates is good for modelling the continental movements (like Pixie and waldronate mentioned) 2) There are two basic methods for generating a "starting situation", either start with a sketch of the "present day" landscape, and start determining the geological history (starting with the movement of the continents), working your way backwards in time, or start with a supercontinent and work your way forwards in time up to the "present day". You can also mix the approaches (for example, start with a supercontinent, work your way backwards to decide how it was formed, and then work your way forward past the supercontinental stage).
Hey, I see that you've done some plate tectonics based mapping. I'm looking to get into that, but am having a hard time figuring out (a) what software works for that, and (b) how to generate a starting set of plates. Do you have any suggestions?? Thanks in advance!!