I guess I never checked to see what others were doing. There is a reason why I have a 0 post count over at KLOV.

I used to have an old flat mail sorting shelf that I got for free that I used to hold PCBs. Then one day I needed wood for a bonfire, and a dedicated shelf for the 8 or so PCBs I had seemed like a waste.
So what I did for most of my PCBs was tape two flats of cardboard together and made pretty much a big old record sleeve / cardboard envelope. With the exception of a few older boards with heat sinks and other things to make them odd sized, for those I used old boxes I accumulated that are in that size, mostly old MOBO boxes.