I'm sort of OCD when it comes to categorizing minis. I have them all sorted for RPG use in baggies, then organized in storage containers.
container 1
Humans - Classes and styles (i.e. barbarians/thugs, armored fighter-type, wizard/warlock, clerics, rogue/rangers, asian influenced, town folk, etc..)
container 2
PC races - elf, eladrin, halfling/gnome, warforged, dwarf, dragonborn, genasi, etc..
Container 3:
Mounts & Familars (any mounted/mount creature and minis associated with familiars)
conatiner 4: Heroic tier Humanoids
Goblins (hobgobs, bugbears, goblins), Lizardfolk, fish people, kobolds, Orcs (separated by class types, as well) etc...
Container 5: Undead, separated by types (skeletons, zombies, vampires, etc..)
Container 6: Paragon Tier humanoids:
Drow (separated by class types), Troglodytes, Yuan-ti
Container 7: Giants, Titans, Trolls, and Ogers (separated by types)
Container 8, 9, 10: Magic beasts, Vermin, Animals
Containers 11, 12, 13, 14: Planar creatures (shadowfell, feywild, astral, Elemental)
Final container is Dragons, separated by color.
Every bag is labled with type, and placed in a larger bag for race (drow, for example), then placed in the container labelling what creatures are in the container.
Makes it very, very easy to find what I need on the fly.