Everyone has their favorite. For me, I prefer the plastic containers that are available from Costco, Home Depot, Lowes, etc. Many of my freight cars, mostly 40 footers, are highly detailed Atlas, Weaver, Red Caboose, Sunset 3rd rail brass, Lionel scale cars, etc. These have separately applied hand grabs, stirrups, etc and I am really careful to protect these.
The first group of photos show the Costco box. I built a wood divider for the bottom with padding on the side and ends. I also screwed pieces of wood to the side that are slightly higher than my tallest engine. The bottom holds 3 engines, the largest is my Lionel scale SP 4-8-4. I then made a plywood cover to fit over the bottom row with a hole in the middle, used to lift off the cover. I can add 6, 40 ft freight cars to the top layer. Everything is protected with bubble wrap and foam padding.
The second type of container with the flaps, came from Home Depot. Same idea as the one above it.
I needed a container for my 18 inch passenger cars and for my larger E7's, E8's, Dash 9, etc. Because I did not want to mix passenger and freight in the same container, I decided to go with a low profile container. So I have several of the same type for easy stacking and transporting.
I do have some standard 40 ft freight cars that do not have separately applied hardware. For these, I use a cardboard box made by Uppa Valley Lines. Since these are not highly detailed, there is little chance of any damage. Uppa Valley boxes are offered by my club member and good friend.
If there are any questions on how I made my containers, please let me know.
Ray