I do it with a brown watercolour pencil, but I guess there are lots of methods ^^. Depends on your own style and preference.
European dealer for Captured in Glass doll eyes Flickr|Ipernity "I suspect Evelien doesn't go around wearing a little white lace hat and wooden shoes." -cirquemom
I'll second the water color pencil. Works and looks natural. Be careful if you seal them though not to brush across the freckles, but carefully dot. You could smear them.