I just try to keep it looking like this most of the time. If I clean up after a project, it's way easier than a massive reorganization after working in a mess for a long time. I can't stand working on a bench covered with junk. It's also a ton easier to work if you don't have a ton of stuff that has nothing to do with the project at hand covering the workbench.
Small parts in the drawers, larger stuff is in the labeled plastic bins below.