There are two free pieces of software that I'd recommend (sort of): GIMP and Inkscape.
GIMP is a photo editor that is similar to Photoshop. It is far less capable that photoshop, but it is free. It is a raster editing program, which means that you control each pixel.
Inkscape is a vector graphics editor. Vector editing is more difficult to learn, but it has the advantage of being able to infinitely zoom in and out. Inkscape can import regular images as well (however, it can not edit them).
The feature that you really want to learn out to use (in GIMP, Inkscape, Photoshop, etc...) is layers.
Commercially, there is Fractal Mapper, Dundjinni, and Campaign Cartographer. They tend to be more bent toward fantasy games than Shadowrun.
My preference if for Inkscape.