I use clear plastic "tackle" cases. Each case is about 9" long by 24" wide and more than tall enough to hold a standing spool. It comes with separators that I can put in. I can get about 40 spools per case. I have 5 cases currently. One holds nothing but my Aurifil 50wt which is what I use the most of. Other cases hold my quilting weight threads (30, 28 & 12), and another with "odd ball" threads (60wt, metallic, clear, etc) ... etc. I label the front of each case. I also keep my thread notes (ie needle size and tension that works best with each thread) on sticky labels on the inside flap of the case.
I have a small book case in my sewing room where I keep them stacked along with my sewing books and store other notions.