I use the stacking plastic drawers available everywhere. I got mine from Walmart. One drawer for each color family with a sticker on the front. Greens, Blues, Reds, Yellows, etc.
I would rather put money into thread and fabric rather than fancy storage units.
Yep i took that idea and ran with it...word of advance, I used a hot glue gun and if you are to rough or try to put to many in one space the glue breaks off. I love this idea but I think it will be revised to just card board spacers, I am thinking you might be able to fit more in. This is my main thread storage but I have 5 sewing stations set up in this rm so i have alittle thread stored at each machine.