In the eternal quest for thread storage, here is what I am using now. I found clear stackable storage boxes at Hancock's Fabrics. Each box holds 15 spools of thread and I am able to have one box per "color family." If you do not have a lot of wall space for the hanging spool rack (which I also like) these work nicely.
I have a small cabinet with several drawers that sits next to the sewing machine. I am able to get 4 of the spool boxes in each drawer and can tell at a glance if I need to go and buy more thread.