I used to have it by type + alphabetically. My binder starts with my Victory Medal :3, then my shinies, secret rares and such, then my Lv. X cards. Then there are some other things of random value (Vaporeon and Flareon Star, Gardevoir EX SS, etc
and then it goes into type - colorless first, and then the next type is whichever trumped the previous one (so fighting, then psychic, then dark, then i get stuck and switch to metal, then fire, then water, then electric).
Inside types, it's pretty random. I SHOULD get a second binder for rarer cards, sounds like. And go by collector's number. But, it's such a pain to re-order them when you get a new one...