I used to have things organized by and a separate shelf or area for: show/movie>character>Chronological Order of character's outfits>etc.
Now that I have been slimming down my collection, I have pretty much condensed about 5 lines of action figures into two curio cabinets and gotten rid of anything large such as ships and vehicles when possible. They have just been falling into place along the way, with no real order.
Once I am done separating "keepers" from "sellers" then hopefully I can have a slimmer, trimmer, collection.
I learned being a completeist gets you nowhere but broke and stuck with some stuff nobody else wants.