Ours are in clear tote bins, somewhat organized by project.
At the quilt show in Knoxville last month we purchased several cards from Polar Notions (www.polarnotions.com) to help us store fabrics. You wrap your fabric on them and they keep the fabric folded and neat. You can put up to 15 yards on one card, so you can put all of your fabric for a specific project on one card and keep it together. We have some organized by project, some by color, and some by pattern.
The cards are 12" tall and fit on most bookshelves. They are heavy enough to last forever and designed very well. I highly recommend them.
Darren