I've tried everything imaginable to store thread in a way that's visible, handy and orderly. A few weeks ago I was walking through a Lowe's hardware with my mother and saw these boxes. They have turned out to be the best option I have ever tried. You can see that the large spools fit perfectly into the molded tray. The smaller spools look sloppier but the box still functions well for them.
This isn't all my thread. The large cones are in a box along with ziploc bags of specialty thread like heavy duty rug thread and jeans thread (yes, J. P. Coats markets that weird orange thread used on jeans). I have another bag of hand quilting thread, which I don't have very much of - that will probably change as I try my hand at it more.
Some of this thread must date from the late 1970's. See that teal thread on the small gold-colored spool? That was from a suit I made for my mother. The large spools of pale yellow and pale green are from chintz drapes made for my bedroom and the guest room about 15 years ago. The little gray spools of Molnlycke thread were bought to match colors used in my in-process Baltimore Album blocks. It's fine for hand sewing but I've never owned a sewing machine that could tolerate it. There's a lot of pinks because I went through a Moda/Robyn Pandolph phase, and a lot of different beiges and taupes. There's almost no red, or orange, but there is a spool of peach. (Yikes, what did I make that was peach?)
There are so many kinds and weight of thread out there, and I really don't know anything about them. I have three kinds of thread - Coats, Molnlycke and the large cones (forgotten the brand name). Someday I need to catch up my education on thread.