Organization is an ongoing shop problem, at least for me.
For small screws, nuts, washers, etc., of which there seems to be at least a million variations, I bought about a dozen of those multi-compartment plastic parts boxes, about 4" x 8", from Brownell's. Each compartment in the boxes is about an inch square, but that's big enough for 4-40, 6-32, 8-32, etc. I made a set of shelves just big enough to hold the boxes, two stacks of 6 boxes each, using 3/4" plywood for the sides, notched to take shelves made out of pieces of Formica. That takes care of a lot of the bits.
For larger stuff, I bought a set of metal parts boxes -- metal boxes with interior plastic compartments -- that hold the larger nuts and bolts, dowel pins, and whatever.
For taps and dies, I got one of those 60-drawer plastic organizers at K-Mart. With 60 drawers, I can go from 0-80 to over 1/2", with a separare drawer for coarse, fine, and "special" for each thread size.
I still don't have a good storage system for raw material. I made a set of narrow shelves under my bench, about 2" high by 6" wide, that hold drill rod and other bar stock, but the shelves are "end loading" and short stuff can get lost at the back. It would be better to have a lot of narrow "side loading" closely spaced shelves, but I don't have a good place to do that.
Try to make a living, not a killing. -- Utah Phillips
Don't believe everything you know. -- Bumper sticker
Everybody is ignorant, only on different subjects. -- Will Rogers
Law of Logical Argument - Anything is possible if you don't know what you are talking about.