I have the lovely inconvenience of needing to hide mine from my nosy roommate -mom. So i use a bag hanging on the back of my door where i know she won't look. Tuck them inside and throw a hoodie on top inside the bag, zip her up and i'm good to go. ;D
I keep my metal toys in their original boxes, my glass toys are in the padded pouches from Don Wands, and my silicone toys are in small lint free cosmetics bags. Plastic and TPR toys live in Sugar Saks, which are antimicrobial. Everything is then carefully stowed away in locking containers such as the Tunti and the Devine Playchest.
Everything is in its original packaging in the bottom drawer of my nightstand at the moment. I will eventually get rid of the product packaging on a few things, but for now, I don't have any alternate packaging and I don't want everything in Ziplocs.
I'm planning on making my own padded bags for my glass items, then I will make zippered pouches for all my silicone toys.