I purchase clear plastic boxes from Joann's jewelry making section when they are on sale, or I use a coupon. There is two types, one w/set plastic compartments that will hold the large C&C threads, and another type that have dividers that can be moved around to fit other sizes of thread, also good for bobbins, and other accessories. They rarely cost more than $1.99 and when on sale .99.
I envy those of you who have a whole room for your sewing, in Texas we have a 4 room house and since we each have our own bedroom I have had to keep sewing table, etc. in my room. DH is going to have a shed built just for my fabric, (stored in large plastic totes and labelled. In Illinois I have a larger house, again separate bedrooms w/the third used as a computer room w/book shelves. I sew in the dining room under a sunny window and all my stash is organized on the closed in front porch. Since I also bead and crochet my stash is large, don't know what I will do when we sell and move permanently to Texas.
Some good ideas here, I like the fishing tackle box idea and the foam ear plugs idea.