I like the actual "bolt bins".
I have a couple of the 72 hole versions
McMaster-Carr
I also have a bunch of the plastic bins like shown in post #6. Use them for small items.
One is full of taps
One is left handed drills and extractors
One is full of sheet metal screws and lags
One for anything smaller than 1/4" bolts, like all the machine screw nuts and bolts
One full of electrical crimp on stuff, like forks, eyelets, blades, butt connectors, etc
One full of brass fittings. Compression fittings and barbs
I got them at HF, cheap and effective. If you get some of those, get more than one. You can interchange the bins inside to better organize stuff if needed. I have one that is full of all the really small bins. Thats for the electrical stuff, since you can get alot of them in each small container. The one with taps is mostly the larger containers. But its nice they are customizable