I'm blessed with the services of a seamstress, often for trade. She's made me a great sturdy upholstery material tote with flat reinforced bottom and crossed straps so when you lift it, it doesn't pull in toward the top, mashing things together.
Into this go my current working decks in bags that have been custom made for the theme or personality of the deck, so that at a glance I can pluck it from the tote. (ie. Housewives is in a red-and-white checked bag with strawberry shaped bead pulls, like a picnic from the 50's.)
That said, I keep every box and its entourage in a special armoire, away from dust, light, etc. Hard to imagine ever selling off most of these beauties, but if ever the day comes, they will be lovingly repackaged and carefully sent (probably with their "dress" bag!)