Of course, when you are buying online you have to order enough to justify shipping - right?! So I now have quite a thread stash.
I store my perle cotton threads and hand dyed threads in plastic bins. The handiest one I have found is this two sided bin in which I store my Prescencia and Valdani threads.
I store my DMC skeins on stitchbows in binders. I have the entire 400+ range of DMC colors stored in 6 binders which fit neatly into one Snap and Store file box. But of course I have extra skeins of some colors, those I store in small craft cabinets. I do not use bobbins. I don't like the folds and kinks the edges of the bobbins make in the thread.
I use a Plano 20 gauge ammo box to organize my Kreinik and other metallic threads.
I use a Super Stacker plastic bin store my specialty threads and cones. I keep my silks and specialty threads in Floss Away or snack sized bags.
I use a bobbin box to store my Nymo beading thread.
All of these storage containers are stackable and sturdy. It really helps keep my every growing stash of threads contained, clean and organized.