I keep like items together: Kaffe's, b & w, batiks etc. It's not perfect, but fast and easy.

I also use the plastic shoe box size totes. I labelled the front with the appr. size for each tote. Also keep my fat quarters in these totes by color or type of fabric........such as batiks. Keep my orphan blocks and certain cut-offs in these totes in case I want to use them for a border or sashing on a project. Not much gets tossed out.