I discovered a set of storage units at Walmart a while ago. In essence, they're just deep plastic drawers that pull out of a unit, and each unit can be stacked on top of another. Each unit has three drawers, and I stack the units three high. This has provided ample storage space for my materials. My tools stay on my tool caddy, and my threads and other spooled materials stay on my thread caddy.
Of course I'll eventually outgrow this system, especially since my wife is getting into the tying pretty heavily now. At least I can count on her to occasionally replenish material stocks as she uses them.