How to restore minifig faces
If you have a steady hand you can use hobby paint or a Sharpie, let it dry, then put on a clear-coat for protection. But those heads with the classic smiley faces are so cheap on BrickLink, you could just replace them. Here are the Catalog listings for the original Classic Smiley on BrickLink along with the dates of production: 

Hollow stud original from 1978-2013: http://www.bricklink.com/catalogItem.asp?P=3626bp01

Solid stud from 1991: http://www.bricklink.com/catalogItem.asp?P=3626ap01

Stud recessed from 2009-2014: http://www.bricklink.com/catalogItem.asp?P=3626cp01