It depends on the nature of the scratch. I have sucessfully touched up parkerized guns with a dark finish using Birchwood Casey's Super Blue on a Q-Tip, lightly moistened. Too much and you'll just get a brilliant blue scratch instead of a white one.
I've used the same procedure on Glocks. The scratches completely disappear! The hardest finishes to touch up IMHO are light grey parkerizing and polished blue. Anything you do to it will stand out.