Terry,
My standard operating practice is to clean up after every project, unless the project is a large one. And then, I will do a pick up in the middle of it. I hate nothing more than to spend (waste) time looking for things. I also like workbenches I can work on without having things in the way. Keeping a clean work surface just makes playtime some much more enjoyable.
You are also correct, that if you let things go to far the task of cleaning up is huge. Another key to this issue is resist being a hoarder of things, something I think that we all can identify with. And if you are going to keep that item, find a proper home for it. I just have to realize I just can't keep everything.
The next trick particularly in organizing is attacking a huge organization of a shop. The trick is to attack it a little at a time, piece by piece, and to stay at it until completed. I love being in my shop and even the act of organizing is very enjoyable when you know that the finished outcome will be fantastic. Organizing is a thinking mans game. Sometimes certain areas can get reorganize a couple of times until I get it right.
Terry, you have a great shop that you can always be proud of.