Mine are mostly for 28mm game play so I've taken to building as many to be "Fold Flat" as possible so I can store them in plastic bins - this applies mostly to buildings. Also I have lots of wall and corner segments for assembling buildings and dungeons on the fly. But a few, especially sailing ships and complex architecture such as buildings with interiors, I store either in deep plastic drawers or out in the living room on our shelves. Though it has started to draw attention from people who don't know that I have this hobby...
The Container Store > Like-itŪ Modular Drawers
