I store the very few jelly rolls I have in a basket on display in my sewing room. I store my 2.5" and 2" squares in divided silverware trays from the thrift store. They fit perfectly in the sections and I can sort by color per section.
I bought one of those 10 drawer roller stands at JAF when it was on clearance and I keep all my other sized squares in there, one or two sizes per drawer. Being a scrappy quilter, I cut my scraps into the closest size square I can.