If you haven't seen Adam Savage's "Sortimo" system, then you might not want to... because after you see it, you're going to want one of your own.

Unfortunately, each box is on the order of $75-$100 and I can't imagine what Adam's entire rack cost. See his setup here:
https://www.youtube.com/watch?v=1OPSbF6kM9k

Harbor Freight, sells a knockoff box, that while not perfect, does the job nicely. Unfortunately, each box comes with a preset assortment of bins:
http://www.harborfreight.com/19-bin-portable-parts-storage-case-93928.html
(There are also larger, double height sizes, and a half width smaller size as well)

I wanted more small bins, so I decided to print my own. If I design other sizes, I'll add them to this thing.

UPDATE I recalled this person on garage journal used a bun pan rack to house his Harbor Freight boxes. I decided to do the same. I couldn't find a second hand one, so I just bought a cheap (~$100) one from eBay. Luckily, the cross rods on the rack I purchased were an extrusion that made it easy to cut to length, and re-tap. No additional materials required.

My first attempt was printed upside-down.

Remove the lip with a razor (it is intended to help hold the part down to the bed
I have more work to do to find the optimal design and printing method, but this initial attempt works as a start.