Lot's of great tips here, I have been using some of them already.
My tips include using plastic peanut butter jars for storing fasterers, you can screw the caps into the bottom of shelving to free up space and, being plastic, if they drop, they won't break...I don't know how many baby food jars I broke in my lifetime.
Using a mini clear tackle/parts box with a locking lid to keep all those small drill bits in one place.
If you have metal wall cabinets above your bench, place several magnets on the doors and allow them to hold your wrenchs, plyers, and hand tools when working on equipment on the bench...no more searching for tools buryed by the part on the bench, they will be at eye level.
Another use for earth magnets is to place on on your oilpan next to the drain plug...remove just before changing oil and all the metal particles will be the first things flushed from the pan.
Cut a 1/2 PVC drain pipe into a 1' foot section and screw under shelve to store doll rods, threaded rod, or tubing.
I have a lot of spray type bottles for detailing my cars. I strung, with bailing wire, a long clothes hanger rod horizonally along the garage, about 61/2 feet from the floor and store all my spray bottles on the rod.