I am also in the plastic shoe box camp. They are a great asset to a shop.
For things that need other shape containers I try to get groups of boxes the same size and shape. I do this so they take up uniform shelf space.
As you can see in the pic of the 22" deep cabinet with the boxes, deep shelves STRONGLY tempt one to put stuff in front of the boxes. So I violate Glenn's wishes for shallower cabinets so nothing can get placed in front of a container. However, there is usually room to move the ONE thing in front of a box to another location on the shelf so it isn't as bad as he thinks.
In the late 50's I built a medical building. My suite was twice the size of a typical optometric suite. There was enough room that everything had a place. That made it very easy to put everything away every time. My shop is about half the size that it should be; storage is a problem. That means that a lot of things are in the "for now" location.
When I wrote "everything" in the above paragraph, I really meant "everything," every screwdriver, nut, screw, med bottle, lens, frame, patient's file, text book, etc. Nothing was ever out of place; it was easier to put it back where it belonged. Oohh I long for that in my shop.
First of all you have to be smarter than the machine.