The ones that came in blow molded cases stay in them. My main set was a great large craftsman set that my wife, fiancée at the time, gave me as a gift.
All the rest are on metal rails. Not the biggest fan, but I can stack them and drop them in a drawer a drawer or bag, and keep lots of stuff together. Those flat organization trays are nice if you have endless space or want to keep it flat. Not helpful if I want to take stuff from my basement to driveway or garages.
So I find the metal rails to be the best. Not fancy or pretty. Just useful.