Many years ago I would get 120 negatives processed and a roll contact made. So 1 full length of 120 in a plastic sleeve with 1 equivalent length of paper. Would come in a box about 3x3x3 (like these: http://www.boxescheaper.com/gift.html). Convenient for storage as they would stack and could be labeled, but very inefficient as a lot of air space in the box. I'm sure you could get a 2-3 rolls in a box without having to wind it too tight.
I would suggest some sort of wood or plastic tray to store them and stack them.
You could cut plastic or aluminum tube but then tougher to stack and a lot more work and/or expense.
Printfile does (or did) make roll negative sleeves (1 long roll - cut to length). I think I still have a box around here somewhere.
Another alternative might be to find an old map/blueprint file (wide but short drawers) where the full length could be laid flat.
Great ideas everyone. Thanks - looks like we've got a couple of workable options.