I don't know if anyone's tried this on a real map, but in theory OOM makes this dead easy with its native .omap format - which is just XML.
If you started with the same base map, which has the same colours and symbols, then the actual map data is just a collection of tags:
<object type="1" symbol="99"><coords count="46">-106940 36850 1;-107700 36870;-107700 38040;-108460 38060; ...etc...;</coords><pattern rotation="0"><coord x="0" y="0"/></pattern></object>
Any good file comparison program, eg.
WinMerge for the windows junkies, should be able to merge two or more of these files without even blinking.