I used plastic boxes that were about 16 x 10x 7 inches. I put them on their sides on the shelves which made it easy to pull a box off without having to dig it out from under something. Also the boxes are not truly clear, but you can see what colors are in the box without taking the lid off.
Here is the link that shows a picture of what I'm talking about.
http://www.quiltingboard.com/t-33984-1.htm
If this is interesting to you, PM me--I've since change my method and have a bunch of empty boxes you might be interested in.