Son-of-Shem   
Guild Novice

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).

Hi there.

You will need to draw a lot and write notes on top of those drawings, so anything that will let you draw using layers is indispensable (gimp, photoshop, krita, etc).
Then you need two more handy programs - g.plates and g.projector. Despite the similar names, they have little in common. G.plates is an academia piece of software to draw "plates" in a sphere and visualize their movement (spherical movement is difficult to imagine). G.projector is from NASA and allows you to create maps using many different projections.

As to the starting set of plates, anything goes, as literaly anything will be changed so many times before you settle into something you like. There's a couple of threads going on now, with tectonic starts, why don't you just join the conversation?

Search for g.plates here at the guild and on your favorite search engine. You should get a world of information and suggestions for resources on plate tectonics.