I guess that's one advantage of my (otherwise bad) habit of posting each chapter as I complete it - I never have to worry about losing WIPs (unless AO3 goes down, heaven forbid). Also I do all my fic writing in Evernote, so I don't even have to bother with local copies. It's probably not the "best" system (so the extent that one can objectively say any system is "best"), but it works for me.