I have two small-medium plastic bins from Chez Target. One holds what I need every single time I go on a trip: medical kit, tool kit, kitchen kit, "junk drawer" bag for misc. stuff, stove, headlamp, and so on. The other holds replenishables and optional items: spare Aloksaks, trash compactor bags, fuel canisters, extra containers for repackaging food, et cetera. Bigger items - packs. bear canister, sleeping bags, yadda yadda - are all in a closet and not especially organized due to size. Ditto with clothing.
My gear is mentally further bifurcated into summer vs shoulder-season items, and solo vs group supplies, but not grouped as such.
Not at all finessed, but the "always-take box" approach has prevented me from forgetting essentials all year! That and, um, that gigantic and anal Excel spreadsheet I review three times before leaving the front door. :-)