Well--not being the queen of organization---in my sewing room the thread is sorted by color into large mouth canning jars and those and the larger scraps (1/4yd +) get stored in the top of a china cabinet. The bottom holds wools, my fusibles and some tools. There's a trundle bed in the room (covered usually with works in progress) and the trundle has no mattress but does have some bat and some fabric (wide backs and future I Spy fabrics) I also have some of those plastic drawers full of smaller scraps and patterns.
In the basement long arm room, I use a closet with shelves to hold tools and pantos, rulers on a pegboard (I do this upstairs too) and have 3 footlockers full of thread cones, sorted by color and each kind/color together with left over bobbins, in plastic baggies. Both rooms have window coverings that keep the sunlight off of the fabrics (although I'd like to be able to look out the window!).