Thank heaven for zip lock baggies. I do quite a bit of applique so have a couple dozen types of thread of every color I can find. Each color goes into a ziplock. Ziplocks go into a small bin (about 12x18x10), but that is just lately, not enough - going to have to get another bin.
The threads I piece with are on a large wooden rack with dowels ( I use a drinking straw over the dowel to stack the spool and bobbin together. My quilting threads are there also. I use Magic Tape (the clear stretchable stuff) to cover my threads to keep them clean and the ends tucked away nicely. I keep the rack next to my machine for quick access.