A word of warning: If you decide apply black paint. You should absolutely use water soluble paint -- or you will be very sorry when the solvent within the paint wicks into the balsam holding the lens groups together.
I found that calligraphy ink or something similar works quite well. Since there is no physical stress on the elements after you've put them back I had no issues with it flaking or rubbing off over the years.
That all said, I found the blacking to be more of a cosmetic issue (it is indeed unsightly) than anything that affected the imaging quality of my lenses. Even in very bad cases.
