Some I keep in a box that I use when I am working on a sewing machine (I sell a lot of old sewing machines...), that way I can see how it is stitching and make samples using the different attachments.
I don't like the ones that are all kinds a shapes so I straighten them up a little with my rotary cutter and put them in another box. I sometimes seperate them by color or theme, keeping all kids fabrics seperate. I keep the cottons seperate from the flannels too.
I have an old buffet in my basement I use as a cutting table and I store lots of scraps in the drawers and UFO's in the one side door and stuffing in other.