Picture of Workbench under-shelf jar storage
I was tired of having a pile of screw and nail boxes, and had more than a few collections of nuts, washers, and other bits of hardware and odds 'n ends around my work area that needed a home, so I collected a few jars and made this under-shelf storage system.

My father told me about this system a while ago- his father had had it in his shop. I installed it for myself, and it has made things SO much nicer and easier.

Step 1: Materials: Jars (duh)

Picture of Materials: Jars (duh)
You can use any old jar, so long as you have room for it. Smaller jars (like baby food jars, as my grandfather used) are probably best. For one you can fit more of them under your shelf, but really most hardware doesn't actually need the space of larger jars (like the two tomato sauce jars I've got in the picture).
I also use peanut butter jars that are clear plastic. I made some shallow shelves under my cabinets over the back of my workbench and this makes stored items readily accessible. Other types of clear plastic jars work equally well.

I'm in the process of changing all mine to plastic peanut butter jars, they tend to bounce rather than shatter on those inevitable occasions when a jar works loose or you don't quite do it up properly; they need a little extra support in the form of large washers or a metal disk cut from a can but the extra time is worth it.