Generally speaking I put anycards valued at $10 or more into top loaders with soft sleeves. Also most HOF RCs will go into the same holders. My sets are in set boxes with a key card or two sitting on top in top loaders.
From there it is a real mish mash. Some star cards are in notebooks, some are in 800 ct boxes, some are in 5000 ct boxes with soft sleeves sorted by player.. Most vintage commons are in 800 ct boxes snugly packed with protective material. There really is no rhyme or reason for my storing methodology, except for my $10 and above rule. It seems my cards were stored with whatever supplies I had a lot of at the time. If I had a lot of notebooks and pages, the cards I was sorting were stored in those. If I had a lot of boxes, they tended to go there and on and on.
Along the same lines, my storage question is how people store their GU cards that are thicK? I am having a real problem figuring out how to protect and store themsince many are too thick for sleeves and top loaders.