If you are using Blender you can do quite a bit of stuff when it comes to mapping. I've used it before not for 'mapping' per-say although I did take a relief (normal) map and made a 3D rendering. This can be used as a bases for your map.
I didn't know there was a place here for that though.
With a bit of work you can create quite a bit of stuff with 3D software. From a mapping standpoint though you will be working back and forth 2D and 3D to get the map to look as you would like it too.
If you aren't picky about how your location will look. You can use a cloud filter to start with in your 2D software and then using Blender you can have your 'normal' map deform a mesh then you can add your water table till you get the land form you like. After lighting the land form you can then export that rendering back to a 2D program to complete the process. That's what I did anyway. You can of course do the same thing in a 2D program but with the 3D you can make changes faster and can adjust if you want to later. You can as you have the same structure in both 2D and 3D add other elements to your 3D map (buildings and trees). There are even plugins to help you build cities (streets and buildings) if you like. You can work in perspective or orthographic. Orthographic would make a better map as that doesn't work with vanishing points.