Another doofus up in this biaatch! :p
For me it makes absolutely no sense to organize by region and/or medium.
Isn't the whole idea of organization to keep things neat & easy to find?
I don't know about anybody else, but when I want to play a game, I have a real good idea in my mind going in what game it is I want to play.
I'm not thinking,
"Today I want to play a Japanese HuCard by Hudson that sports a pink 'HuCard' logo on the spine!"
or
"Today I'm gonna beat one of my SuperCDs, but CD-ROM^2s are definitely OUT!"
or even
"Let me pop in a US HuCard game that doesn't have an orange spine label!"
For me, when I get the irk to play a game, I'm thinking
"I want to wear the Nova Suit in Keith Courage!"
or
"The Bydo Empire doesn't stand a chance against THESE guns!"
or even
"Oui Oui Jumbo is a PANSY!"
And then I can quickly find my game of choice because my games are all lined up alphabetically. I'm not wasting precious time I could be playing said game worrying about silly subcategories and pink & orange spine labels.
That is why anybody with overly elaborate organization schemes is a doofus, or possibly just a super-geek.