This has been a great thread! I have tried a number of methods (bins, stacking etc), but I think the mini-bolt method (like quilt shops) mentioned here will work best for me.
I do use small see through storage boxes for my projects in progress or in-waiting. Sometimes if I'm not into sewing, I'll cut a project so it will be in kit form later on. I include the fabric with any special notes and place the pattern on top.