AutoTileGen is software for generating terrain-based tilemaps from 3 input images. For example:
These 3 images:
Resulted in this tilemap:
Which can be used to make maps like this:
This attached annotated capx shows how to integrate the generated tilemaps with C2's tilemap plugin.
07/28/15 Update: AutoTileGen v2.0 came out a few months ago. It has some very nice improvements, but the order of the tiles has changed when exporting. I've update the attached capx, and 2nd image above to reflect the new order. The capx will only work on tilemaps exported in v2.0 or later.