It's more or less manual, with GIMP, using/tweaking the following tutorials -

RobA's original tutorial (for everything up to mountains): "Using GIMP to Create an Artistic Regional RPG Map" http://www.cartographersguild.com/tu...l-rpg-map.html
And the revised, 5 part PDF from this thread: http://www.cartographersguild.com/tu...sentation.html

downloaded from Forums->Tutorials/How-To->Tutorials in PDF Format:
"Making Photorealistic Trees in GIMP: A Mini Tutorial" by Arsheesh
"Simple Mountains in GIMP" by RobA

FYI: After hours of experimentation, I found that by mixing-and-matching/tweaking and playing with parts of each tutorial, I can USUALLY get what I want; tho I still can't figure out how to make a decent volcano.

Hope this helps.