As a team collector, I've been organizing my collection while laid off. The way I do it is to store my best copy of each card (assuming it's not encased) in ultra pro platinum pages and then store them generally in binders. I don't really like traditional 3 ring binders. When I was younger and collecting, I purchased (no idea where) 3 or 4 binders than were 1.5 inch D-ring binders enclosed in a hard plastic case, so the cards are completely protected. I use these for my more valuable team sets. I've been looking to find more, but the only ons I can find these days have round rings instead of D-rings, and I'd really prefer the latter. On an added note, I don't stand the binders vertically--I lay them flat.
My duplicates are generally stored in penny sleeves inside card boxes. Again, something from my youth that I wish I could find. When I was a kid collecting, my dad bought me a few boxes at a local closeout store (been out of business for decades now). They are exactly the size and shape of typical 800 or 1000 card boxes, but they're made of hard plastic. I really like the durability and extra water-proofing these provide. My encased/graded cards are stored in regular plastic boxes to keep them safe.
My for sale/trade cards, cards I just want to eventually get rid of (once i get totally organized--give me another 2-3 weeks and I'll probably be done) I store in penny sleeves inside regular cardboard card boxes.
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