Wrapping them in paper towels are a must if storing in a cardboard box. Placing tissue between cars is a must as well. I just opened up all my boxes of cars from when I packed them away over four years ago. I was amazed at the amount of couplers broken from NOT cushioning the couplers with something soft between cars.
I just finished building a wheeled chest for storage of cars while off the layout. This chest will fit under the benchwork. I used 3/4" ply for most of the construction, with 1x4 pine, some oak, and 1x12, and other board to complete the chest. It also will double as a mobile work area in the train room with the casters on it. It will also fit between my isles when they get built. It has five drawers with four of them using cabinet drawer hardware for easy roll out.
I plan on putting felt on the drawer bottom to prevent the cars from rolling and also help be more gentle on the cars that will be on their side. I'd put a materials cost on this of just around $80 or so. I also plan on using the sides for storage of tools, etc. Once the layout is done, many of the cars will come out and I'll use it for tool and part storage. I may make a fixture for a work lamp to be attached.