I use some of the clear shoe boxes and unused pizza boxes. I have also covered washing powder boxes with fabric and used them. My favorite boxes are the rollable 4 or 5 drawer carts at Wal-Mart.

I have a shoe cube organizer with a drawer at the top for my fat quaters and thread. it's fantastic. I seperated the fat quaters into colour groups and they each got a section. Each spot holds a lot of fat quarters. And then the drawer is were I keep all of my thread spools when I'm not using them. I love it!

Anything smaller than a fat qtr, I usually pre-cut into squares of varying sizes (1-1/2" to 7") and place in ziploc bags.
Whatever you use, you will want clear (Totes, zippered comforter bags, ziplocs)-that way you can at least see it when you walk up on it, rather than having to open every container to check.

I found hanging cube organizers with a shelf in each 12" deep cube- at walmart. So there are then 10 sections per column and 5 columns fit across a regular 6' closet. When I worked at Joann's I bought every remnant available so I have tons. I have them all seperated by color (some by theme) and folded very neatly. I can see everything at the same time.

Thanks for the suggestions, this is helpful!