Jim Williams seemed to have the same problem.
I've seen various images of Jim's bench and I think it has been preserved in a similar state as a kind of shrine at Linear tech.
If you look past the clutter, his bench is actually laid out very efficiently in terms of access to the test gear. Mine is very similar with an L shaped work area, but mine is mirrored compared to Jim's layout. The crazy thing is that it would only take about half an hour to put all those dev boards into some kind of storage system. Then his bench would be very similar to mine, although my test gear is mainly RF stuff. Some homemade shelves would have helped a lot as well. I made my own custom shelves and they have transformed the work area.
To store old dev boards (and I have many...) I use large biscuit tins and then put these inside huge drawers that live under one of my benches. I have storage tins for LNAs, oscillators filters etc.
I still have to spend a fair bit of time battling against the build up of clutter. In my case, it's usually coax cables and wires and previous test boards and various RF adaptors and attenuators that gradually build up a layer of clutter. I try and tidy up most days, but it nearly always looks a bit untidy.
I have a few rules that help maintain a good working area and these rules are:
No hand tool storage on the main work bench.
No component storage bins on the main work bench.
No more than a few old dev boards allowed on the bench at any one time
Only a few items of test gear live on the bench all the time. Most of it is stored like sardines in another small box room and I only retrieve it when needed.
Always leave some shelf space clear and always try and put away stuff that won't be needed for a few days or so.
This lets me fit three work benches into my small work room and on a good day they can all be fairly free of clutter.