Some might find this video useful. It's a little long and the technique described is somewhat time consuming, but if you're a perfectionist I think this is the route to go.

https://www.youtube.com/watch?v=PBgdVfiE5EI

I'm re-finishing a 100+ year old low dresser and am at the point I need to fill the 100+ year old nail holes. The original material that was in the holes fell out or disintegrated long ago.