Well in the past I've used pencil. But after reading the thread on Photo.net, where someone suggested trying a red sharpie felt tip, I gave it a shot. But first I located a water soluable one, just in case I didnt like the results.
I had a hole in the neg, of course smack dab in the middle ofthe sky. I touched it with the red felt tip and printed. Sure you end up with a small white fleck, but that is easily spotted using spotone. Overall, it's a method word dabbling in. ;-)