I'm in the process of cleaning and reorganizing my sewing/quilting room as I'm writing this reply. It took me forever to get started, too, because I was overwhelmed at the thought of it. So, I just decided to do a little each day, by breaking the job up into small tasks. However, once I started, I got on a roll and didn't want to stop. Here's what I learned:
1. No plastic bags!!!!
2. Keep all of your project supplies for each planned or incomplete project together in one basket or fabric storage container until completed--you can find all size fabric containers for $1 at the Everything's a Dollar store (a.k.a. Deals).
3. Store your new or project leftover fabrics in your stash by color or size or theme (e.g. batiks, novelty, stripes, juvenile, etc.)--if necessary, cut it up by yardage, fat quarters, jelly roll strips, scraps, selvedges, etc.
4. Store all UFO quilt tops together and all orphan/exchange blocks together, so you can find them easily when you need to create a quilt quickly.
5. File, using a Pendaflex or similar file with labeled manila folders, those loose printed patterns, workshop notes, correspondence, catalogs, etc.
6. Use a "graph paper" notebook for jotting down project notes, design ideas, etc.
7. Use large bins for storing battings, fusibles, stabilizers, treated fabrics, etc.
8. Where possible, use vertical storage with peg boards, cork boards, thread holders, etc. for storing small items.
I sure hope some of this helps.