My current setup has a bunch of plastic storage units with drawers for pre-painted plastic minis. I have the following drawers at the moment:
--Demons and Devils
--Angels and Elementals
--Giant Humanoids (giants, ogres, trolls)
--Monstrous Humanoids (human-sized, humanoid monsters that don't belong to one of the orc/goblin races)
--Constructs (golems, animated statues)
--Humans ("generic" humans that come in groups, e.g., archers, footmen, cultists)
--Orcs and Goblins (orcs, goblins, hobgoblins, bugbears)
--Undead
--Animals (real-world vertebrates, plus giant varieties of same)
--Vermin (real-world invertebrates, plus giant varieties of same)
--Miscellaneous Heroes (unique humans and members of other PC races; players who don't bring their own minis use these)
--Miscellaneous Monsters (any monster that doesn't go in any of the above categories)
Since some of the dragon minis are way too big to fit in drawers, dragons go on top of the storage units. Painted metal minis are on a separate shelf so they don't get knocked around as much.