I just stumbled on this today, and I think it might be of some use. Jamie Hyneman gives a tour of the Mythbusters shop, and if you've ever seen the shop (and who hasn't?) you know they have lots and lots of things to keep track of. Lots of good ideas in here. They have "stations" set up throughout the shop, essentially a place you can always go and find a sharpie, pencil, calculator and tape measure. They've also got a former card catalog used to hold various motors, solenoids, and things. Neat ideas, and as you'll see, everything has a place and its all labelled.
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Part 4