I consider my stipple portraits to be realistic interpretations of a photo, and since all details and tones are included in the drawing, adding color is not necessary. The process turns a nice, b&w portrait into a muddy, brown mess and to tell you the truth, looking at some color stipple drawings out there, I haven't seen a good one yet.
But, since I get asked to do this more and more frequently, I have been experimenting quite a lot.
My answer is a more graphic looking portrait, with the black layer behind the color rather than on top. I also have an easy control over the color, to get it exactly to the client's liking.
Here are a few versions on Barack Obama drawing I did for the Wall Street Journal special use.