I have
one plastic toolbox for SAE wrenches, sockets etc
another for metric wrenches sockets etc
another for electrical, meters, crimpers, strippers, tape, terminals and electrical consumables (bulbs)
another for "plumbing", packing gland wrenches, pipe fittings, teflon tape and consumables
One sturdy zip closed bag for carrying to on deck/dock/dinghy jobs. Not waterproof but would probably float for 10 minutes if dropped overboard
One container for sealants and adhesives, canvas treatment, zipper lube, liquid wrench, corrosion proofing.
One under bunk area reserved for oil/fuel filters, zincs, oil, distilled water, impellers, gaskets, gasket material, packing material.
Behind the settee for bigger tools like cordless drivers/drills/buffers etc.
One shop vac stored in the dock box.
One container for rigging odds and end, shackles. blocks, wire and tape.
Lots of other stuff I don't remember.
Basically I tend to store by function - mechanical, electrical, plumbing, cutting, drilling etc. It makes it easier to know where to find things.
Oh and lots of nuts bolts etc.