If you're looking for something that is specifically designed for mapping, the field is pretty limited. AutoRealm is the only one I'm aware of, although I'm sure there are others out there. You might be better off, though, looking into something a bit more general-purpose. For that, I recommend either the Gimp (a free, open source Photoshop alternative) or Inkworks (the same for Illustrator). Or even both, since there are things that one can do easily that the other can't.
Also consider a virtual tabletop (VTT) such as MapTool, which can do some limited mapping, but really serves as a map management system that can keep track of things like fog of war, line of sight, range, area of effect, and so on. I'm not sure if MapTool is still state-of-the-art, or if something else has supplanted it. I hear a lot about Roll20 these days. I think Realm Works overlaps with that functionality somewhat, but in my opinion, the vision-related functions in MapTool are a killer feature that make it worth running even if you have other tools to cover die-rolling or character sheet management.