I buy bins of nuts/bolts at Boltdepot.com. I go through so many bulk just pays for itself over time. I built a cart specifically for the bolt bins and the tap/die sets. I am in these bins every day. These represent the new bolts:
I bought a shelf with card board boxes from Globalindustrial.com. I use these here and at work. I originally had crap spread down a pegboard. One shelf contains a 20 foot pegboard wall of stuff I could not figure out what to do with. Very Very handy.
2 Shelves are dedicated to nuts and bolts. This is where the overflow from the bins, used nuts and bolts, bolts of different lengths etc go. This is indispensable at keeping these organized.