I too use the card boxes and I organize everything by category.
Some of my categories are meats (for pork and beef, etc.), ground meat, poultry, seafood, soups and stews, Mexican, Chinese, on-the-grill, eggs, desserts, cakes and muffins, beverages, rice and potatoes, pasta, etc.
I've got a few more categories, but that's how I organized mine. I bought the separators with the little sticky-uppy tabs to write the name of the category onto.