We use those clear plastic containers. Each has a picture of the historical girl and her name (in her color) taped on the outside. We borrowed these cute portraits from Kurt's website. A separate box each for shoes, hats, food, accessories, and today stuff. We don't have much in the way of furniture or accessories - DH is not so understanding when he sees yet another charge from AG on the credit card. (Me-But honey, we really need it! DH-Doll stuff? Again?!)
Just a word of caution using cardboard storage - make sure it is acid free. We want all our treasures to be preserved for our daughters and their daughters, too.