When I have fabric for a specific project, I will put them in one of the bags I get from the LQS and the pattern that I intent to make with the fabric.
As for other items, I keep my FQs in one location and then I have a pile of 1/2 yd cuts and then a pile of anything over 1/2 yd. I do not have much, so this works for me. I also have a few small tote boxes that I store Holiday/Winter/Animal fabric in. Once again, I do not have much, so this works for me.
Everything else goes either in or on my computer desk that is now my sewing desk.