The simple rule for designing any organization system, whether for tools, clothes, the top of your desk, etc., is: Everything should have a place for it—and the more clearly delineated that space, the better. If your desk is messy right now, it's probably because it's covered in things that don't have dedicated places. It's easy to scoop pens up and throw them into your pen cup, but it's the uncategorizable things—that catalog you think you might need later, a stack of documents that's important but not urgent, some business cards you've been meaning to file—that create the mess. And then you spend time sifting through all of it to find the thing you're looking for.
Delineating areas for objects is also important, and ideally it should be one-to-one. From a design perspective, I don't find dresser drawers very efficient, because they hold stacks of clothes, and I'm invariably digging through three items to get to the fourth. Ditto with toolboxes, where you spend five seconds of rummaging for every one second of grabbing. Multiply that wasted time over millions of tool-wielding workers that get paid per hour or per job, and you're looking at a lot of man-hours down the drain.
To solve that problem, a creative group of property management professionals—guys whose job it is to keep buildings and facilities running smoothly—got together to develop the Mobile-Shop Tool Cart. Through an extremely iterative, painstaking process, they've been refining the design for nearly ten years, by tracking exactly which tools repairpeople use for which jobs, how often they used which tool, and having them record when particular tools were forgotten (meaning the repairperson had to leave to fetch them, a major inefficiency).
The resultant design packs over 400 tools into a single cart. The 100 most-frequently-used tools live in the bag up top, while the next tier of tools is located in binder-like leaves boasting dedicated pockets. Three stackable, lidded boxes at the bottom hold commonly-used repair parts, fasteners, adhesives and the like.
We're not sure where the second half of this video is—it appears to be truncated and the company lists no "part 2"—but it will give you a good look at the system and what the design thinking was: