Mine is on shelves (like in some fabric stores) standing up on the bolts, by color, solids, blenders and then design,then a section for future projects(with pattern). Then I have a section for 'stash to sell', then I have a plastic three drawer cabinet with smaller pieces (under 1 yard) folded and by color. Then I have a smaller cabinet with tiny pieces separated by color.
I also have see through scrapbooking containers with seasonal pieces in it (Christmas, fall, holiday). And more of the same with UFO work in them.
Then I have a paper bag next to my cutting area to hold the little triangles I cut off while making blocks...... I usually give the triangles away since for some reason I don't use them for anything. They are the only thing I hate in quilting.... tiny triangles.