Check out some of my newer maps here:
Expedition to the Ruins of Greyhawk
Exemplars of Evil

OK. So 100% of my cartography is done in Photoshop, I use a Wacom Intuos 3 graphics tablet, and I haven't touched a Windows operating system in 10 years. They carry disease by the way. (Not viruses, DISEASE)

Typically I'll find a decent background/compass rose and work out a skeleton of the layout with brushes that emulate crisp ink pens. I'll go back later and clean them up as well as add ink details. Once I've got a black and white line drawing of the map, I'll start with the color work. Using the selection wand, I'll group sections like floors and walls into alpha channels so that I can create masks with them later. (This helps greatly when your painting) The rest involves a lot of brushwork and texture manipulation that will take quite a while to discuss.

Alpha channels and layers! The best things since sliced bread and cheese.

More to come...