I'm not too pedantic as to record all my decks on paper. I have them organized into a few categories: Ellusionist, Theory 11, Dan & Dave, Kickstarter, Bee casino decks, Misc. Red + Blue pairs, standard bees & Bikes, Misc. manufacturers & special decks, and an assload of cards I don't have enough room for.
I keep them organized in empty brick boxes sideways. Like books.
I need like 10 more boxes, though.