Those Mohawk finish repair markers are great.  I mostly use them to hide scratches but they also work well when you use filler to patch holes.  I keep several different colors on hand so that I can blend the color to sneak up on match.  They even have fined tipped ones you can use to draw in the grain that really help hide patches.  

--Nathan, TX. Hire the lazy man. He may not do as much work but that's because he will find a better way.