i tend to clump by similar use/mood. spice rack has things like 5 spice, ginger, mustard, cumin/coriander seeds together, baking spices together, herbs together. only things i use regularly go into the rotating rack by the stove.
seem to do similar with books. music/musicology/luthiery together, arts/crafts/pens together, cookbooks together.
would love to claim there is organization within but life is short. ;)