One of the deep, hinged JAF boxes, bought with 50% off works for me. I use mostly cones with either 1100 meters or 5000 meters of 50 weight thread. Most are Aurifil thread, although some are from Connecting Threads and who knows where I got the others from. I need the larger size box for the larger cones. When I change threads, I put the thread cone and the bobbins in a ziplock sandwich thread and keep them together in the box. (There's 3 of the boxes...I have bought too much thread.) I do keep the deco bob 90 weight in a smaller box.
FYI.... I'm finding out that I use mostly, black, gray, light & darker beige and white for piecing. I'm trying to use up all the yellow, reds, blues, oranges and so many other pretty colors.