Depending on the application and how deep the scratch is Dr. Colorchip does a great job. Another to consider is the following:
Fix Deep Car Scratches > Chipped Paint Repair > Touch Up Paint Kit
This used to be or still is by Applied Colors. The difference in this kit is the use of 3M putty to fill in the chip or scratch to make it flush before applying the touch up paint. I would imagine just buying some 3M putty to use with a Dr. Colorchip kit would get you the same results.