I've tried a few ways of organizing over the years & feel like the setup I have now works pretty well for me. When I lived in SC, I had a house with an extra bedroom - which of course meant my stash expanded to fill the space! Living in the Chicago area is pretty expensive - we pay 40% more for half the space - so I've reigned in my stash sprawl. Now it's consolidated to this wardrobe shelf, and a fabrics/finished projects box that sits on top.

On the left are a bunch of individual plastic shoe boxes that hold fabrics for finishing and different fibers. The drawers on the right hold supplies, knitting yarn, and framing supplies.

On top of the drawers are my bead containers. The bags on the far left hold my scroll rods and Q-snaps. Below that are some magazine holders. Below the shelf are my painting supplies and DMC thread box.

All my DMC threads go into a plastic box that's actually made for matchbox cars (I got mine in the toy section at Wal-Mart). It opens on both sides, and allows the bobbins to sit upright, so you can see the labels. I have another plastic shoe box full of extra skeins, organized into baggies by the hundreds (700's, 800's, etc).

My specialty fibers are in baggies with an index card & a label. Spools of Kreinik are in one of the smaller Plano boxes.

All my beads (both Mill Hill & for beading projects) are in watchmaker boxes. I love the how pretty they look in their little round containers. Each one can fit 2 packages of Mill Hill beads. (I ordered mine from Lee Valley - I like the large cases of 33mm) The containers themselves don't screw on, so they can pop open (you can pinch the sides of the bottom so the lid fits more snugly). After hearing horror stories of boxes falling down & beads going all over the place, I put elastic bands around each of the boxes & haven't had that problem! :)

I use an under bed storage box for my fabrics and finished pieces. All my charts fit into a plastic file box that goes under my desk. Having these things organized makes it much easier for me to find things and the wardrobe shelf keeps everything (relatively) compact. D. & I dream of a room that we can have our hobby space in. He really likes Lego, which takes up almost as much space in our apartment!