It seems to be a perennial fight to keep screws, bolts, and nuts sorted. I've seen systems ranging from elaborate jar setups to buying divided boxes and hoping they stay where you put them. This is my take on a screw sorting system that fits my needs perfectly.

There are a few design requirements to consider:

I want to 3D print the parts while avoiding having large, long prints
The screws will be in non-connected boxes in a drawer so I can take out only the one size I want and it doesn't take up much desk space
Lids that keep the dust out. It's fairly annoying to have rogue dust and hairs in the screw piles that's difficult to remove
It needs to be easy to identify where a screw belongs when I inevitably find a random one on my desk in a week.
Limited to socket head cap screws for this initial version, it might expand later, but I try to keep the fasteners consistent throughout my project

Finished product first. The row along the front are all M3 socket head cap screws of varying length. There are a couple M4 and a one box of M12 in the second row.

To help quickly identify the screws in the box as well as checking the screw size there is an exact size indent in the lid

To open the lid as well as hold the latch in place there are two springs. The size isn't critical, they just need to fit over the 3mm screw acting as a shaft

3 parts to print, 3 M3 screws, and 2 springs makes for a reliable east to use screw box.

For the less common screw sizes where I keep fewer on hand I also created a split box that holds two sizes and has two separate labels and screw indents on the lid.

All the files for this project can be found over at Thingiverse.

As of publishing this, I've been using these boxes a few years already, and they have made finding the the correct screw much simpler.

Screw Boxes