I have been doing this for about 15 years, and still use the file folders. I do this by family name for each 12 inch file box, then individual folders for each person. In addition, in each box I have a Misc.folder, one for pictures, and one for notes from oral interviews.
I obviously have a rather small number of families, and spouses and children are in the parents individual folders. I have never had the three ring binder method explained to me. It may be much more efficient. I do use a terrible lot of paper.