I use these:
Card House WITH 12 - 800 CT Boxes
These are the one-piece versions of the boxes Pennsy484 was showing above. I find them ideal for traditional sized rolling stock. The boxes are 14" long (interior) which means you can put a Baby Madison or an Autorack in them. For a Madison car, you'd have to get the 930 CT box; it would stick out a couple inches, but that wouldn't hurt anything. These boxes hold steam locos nicely, but diesels won't fit, except for the little Alco FAs. If you need to hold diesels, you can put it into the slot without the separate box.
I wrap the car in a polyethylene bag which I slit open (you could use sheeting, of course, but for me it just worked out better to cut open a bag). It is hard finding someone to sell you fewer than a thousand plastic bags at a time! I got 200 from clearbags.com, 8x18", flat, 3mil. They will just close around a GP, and they are thick enough that you can remove things from their boxes by picking them up by the bag -- even the heavy die-cast steamers.
In these boxes, the cars have to be stored lying down. I find this a great advantage, because the moment you open the box, you know what you have. Other boxes, you are just looking down at the car's roof.
A before-and-after of a table in the basement. Yes, I was using plastic shoe boxes from IKEA for train storage. Not terrible, but there are far better. There were things in that pile in the back that I hadn't seen in a couple of years.
One of the great things about this system is that everything is accessible at once. Things on the bottom can be gotten at without moving things on the top. It really helps prevent your boxed items from becoming "out of sight out of mind". I find myself pulling out boxes and opening them just to look at what's inside :-)
(Worth noting: for whatever reason, there is no volume discount on the "card house with 12 boxes" KIT. But you can get a discount if you put the Card House and the boxes into your cart separately. As far as I could figure, it is most cost-effective to buy 10 Card Houses and 120 of the 800 CT boxes.)