Glass toys go in pouches, silicone and soft material toys go in Ziploc bags. I'm not sure how I will store my steel/aluminum/other metal toys, since I only have one. I think I will keep the packaging (nJoy packaging is GREAT!) but put the toys themselves in something else.
All toys go into this hollow ottoman thing that I have at the end of my bed. I'm running out of room, so, might have to get another one or find some other place for storage.