If you will always be colouring in the same map predefined areas (like counties, or electoral disctricts, for a topical one) rather than arbirary ones, then you might want to consider something simple to deal with like SVG. You prepare the map in a graphics package like Illustrator, save it as SVG. SVG is a XML-based format, so it's text.

If you spend a little time upfront giving the county-outlines a meaniful name or ID ('TX', 'CA') then your colouring-in phase becomes a simple search/replace on a text file, which perl has Several Ways to do.

I believe PDF can be dealt with similarly. If you need a PNG or something eventualy, for a web app, then there are tools around to render SVG to a bitmap format.

Several graphics packages come with pretty decent maps in their clipart, too. CorelDRAW! certainly used to have good outline maps packaged with it.