I have prints that are ready for mounting flattened and stored in print paper boxes, ready for mounting if and when I get around to it. All other prints are just piled up and placed in the closet. I have very few prints from others, so I don't really have to worry about storage for them
35mm and 6x6 negatives are stored in Printfile sheets placed in binders - with the rings/spine up, so the sheets hang down, mind you. Much easier on the negatives.
My 4x5's I store in glassines, and until recently they were just stored in film boxes. A friend purchased some collectibles off eBay, and they were shipped in US military ammo boxes - he gave me a couple, and they hold negatives perfectly, after you shim up the boxes on the bottom, since they're a bit too deep. They're also watertight, which is nice. Using ammo boxes wasn't my idea, BTW - I was at a Barnbaum workshop, and saw that he stores his negatives in ammo boxes...
My 4x5 negatives are all numbered - SYY####.
S = Size - 3=35mm, 6=6x6, and 4=4x5
YY = two digit year. Yeah, I know. Y3K problem. Oh well.
#### - start at 0000 beginning of each year.