hi topcat - if I had a map that needed counters I'd probably use photoshop, put the map in the bottom layer and then add a layer (or more) for the markers. Gimp would work as well, and you could also do it with Illustrator or Inkscape if needed.
There are a lot of markers in here if you search the forum, and I have a small tutorial on how to make simple ones in photoshop. Depending on what you want you might find it here or just google for some - remember copyright issues though, especially if you want to make something professional