I'm currently learning what should be a cartographer/geologist wet dream. Is a piece of software called ArcGIS, which for what I have learned looks like a really fancy CAD oriented towards geologists.
It can definitely create beautiful maps, and while the way to learn it is less than optimal, it offers plenty of toolboxes as well as custom ones that you can import from other sources.
Right now, I'm just learning the basics and if anyone knows how to extract parts of maps using their Python interface, that would be most helpful.
|ArcGIS sample screen, borrowed from: http://www.esri.com/news/arcuser/1012/graphics/blended_3-lg.jpg|