I’ve given up on keeping papers for reference in manilla folders labeled with the project name, as advised by The David. That works fine for small amounts of paper, but when one has stacks of article copies 500 or more sheets high, it just doesn’t cut it any more. I consulted Molly , who seems to have a pretty good handle on hardcopy management, and she advised me thusly.
She uses 3-ring binders to hold the relevant papers, broken up into multiple binders when needed, for things she’s currently working on. They are clearly labeled in large-face type. More extensive references are kept in little file boxes, using alphabetical hanging files. I’d say the file boxes are about large enough to hold two or three reams of paper. They’re something like this, but nicer. I think she gets them from the University book store. I’m in the process of moving my ever-growing collection of papers to such a system, starting with the file folders.