I use a variety of things and spaces to store UFOs:
1. those scrapbooker's plastic expanding envelopes that hold 12" x 12" sheets of paper. They're clear, so you can see inside them, they close with a flap that is held shut with a string tie. Since they have a flap closure, they keep out dust but still allow air to get inside. I use them for orphan quilt blocks, tops that are pieced but not quilted, etc. They stand up in a cardboard box that holds a dozen or so at a time. The box sits under my quilting table out of sight but easy to get to.
2. for really small projects, or projects where I've cut out the pieces but haven't pieced them yet I use those plastic deli food boxes with the snap on lids, they're free and the lids are clear so I can see what's there. These boxes sit on top of the unit where I keep batting.
3. cardboard boot boxes hold UFOs that are smaller than quilt tops, but bigger than will fit in the deli boxes or that have specialty threads or other materials that I need to remember not to use. These boxes often have more than one UFO, in which case, each UFO is folded and then rolled around the loose materials that go with it. The boxes are labelled using painters tape and a sharpie marker. These also sit on top of the area where I keep batting, interfacing, etc.
4. UFOs that I'm actively working on at the moment stay out and are draped over every possible surface in my sewing studio/guest bedroom. Other UFOS that are in various stages of either being cut out, squared up, sandwiched or in the case of wall hangings are in the process of being mounted on foam board and stretchers are kept in my larger studio space (the room next to the guest bedroom) where I have a large table and huge cutting mat as well as my power tools for making stretcher frames.
Rob