I have my SU stamps sorted by current/retired, then mounted/unmounted and then alphabetically by size box. The clear mount stamps are current/retired and then alphabetical. My non-SU stuff (which I have a bookcase full of) is separated into clear/clear mount and wood. Clear are alphabetical by vendor. The wood are separated by vendor/type. Example all my dragon/oriental stamps are together, all my words/phrases, animals, etc., but I also have a whole container of Karen Stolper by American Art Stamps. I basically think in images rather than by event.
Part of my issue is because I have to keep current separated from retired for a lot of my SU swaps...otherwise it would probably be just alphabetically by size box