My tools are not clean, but I have worked with guys who keep them a lot messier. I wipe my wrenches and ratchets down after each use. A little leftover grease prevents rusting. I guess they are well loved.
I have three toolboxes in my garage. Two stacked on top of each other, which is leftover from when I worked on cars, and a small three drawer right in front of the Triumph. The closest toolbox houses all the tools I regularly use on the TR: SAE wrenches, 3/8 drive ratchets with the 1/2 in sockets always nearby. Anything I pull out stays out on a pile on my bench, or somewhere under the hood. When I am done for the day everything goes back in its correct drawer so I know where to find it for next time. Trouble is, when I leave stuff on the bench, I can't always find it while working on the car when I need it. I was just using that 1/2 inch wrench a minute ago.....where'd it go.....oh yeah fell under the radiator. Anytime a tools falls, it lands in the least accessible spot possible....