How do you sort your genealogy files?

Like your other 2 posters stated there isn't an easy or hard fast way to do it. I have several branches of my family where they were long term residence of an area intermarrying with other long term residents. Based on the way you were keeping records in the past until you starting getting all the intermarrying, my suggestion would be set a "rule" for yourself about where you are going to put these people (ie spouse always goes under their spouses file or child always goes under their parents file etc) then on the other files where that person would go either create a text doent for them that states where to locate their folder or create a shortcut to the folder (I personally would recommend the latter)