Hi,
Most of my decks are kept in bags or pouch that I either made of bought for them (all different patterns, shapes and fabrics ; cotton, velvet, leather, felt, knitted or crocheted yarn, flap bag, drawstring bags, all sorts)
The decks that come in good sturdy boxes (ex: Wild Unknown) are kept in their original box, that more often than not I also place in a larger bag to protect the box.
Then, currently, my decks are stored into two cardboard boxes that are bigger than shoebox size.
The first one, easily accessible, has the decks that I love and use the most. The other box is put away beside other stuff on the bottom of my cupboard, and contains decks that I use less frequently, have not used in a while, or have more difficulty to bond with.
On a regular basis, I get this second box out to go through it and try to fish out a deck to rediscover it, or give it another go. It's cool because sometimes it feels like a have a totaly new deck, when I have not seen a deck for a while.
I also have a small wooden box that sits on my table or my nightstand, and is large enough for two or three decks in their pouch, plus a spreadcloth, incense, candle, crystals etc. Everything I need at the same place, well protected, and I keep in it the decks that I am currently working with. I rotate the decks on a regular basis, at least once or twice a month, often more. If I leave town for a few days, this small wooden box is all I take, unually.
And, lastly, I have a shoebox that is well stored behind a pile of jeans and shirts in my cupboard, and that contains all the tuckboxes from my decks, flattened out ; all the LWB and extra cards (the cards that bear the name of the deck and author and all) ; plus the few back-up decks that I have - decks that I love the most and that I felt I needed a security backup copy of, in case I lose a card or something. Plus, two or three decks that are incomplete but that I keep anyway.
That's it !
I hope to find a better storage solution than this cardboard box situation, but for the moment that is what I have. Idealy I would love to keep my decks in a chest of drawers, but I do not have one available for that. Tanga's pictures of her colorful decks on top of the shelves gave me inspiration though.... But I lack the space... I hope to upgrade my storage one day. We'll see.