Most of my toys reside in a toolbox. I don't do anything special for the pure silicone or hard plastic - they won't hurt each other and pure silicone makes up the meat of my collection, so they just sit clustered together in the main section of the box. Other materials get put in individual plastic baggies to prevent them from reacting with each other and/or the silicone. My one glass toy stays in a padded pouch.
I store many of my toys in the original packaging. It makes for easy identification and keeps the toys clean between uses. I have two of the Eden Fantasy tote bags, and my toys are stored between those.
All of my toys just get tossed in one box. I'm trying to buy only silicone and steel so there aren't any funny material interactions between the toys. Lubes and towels are in a separate box and both boxes are under the bed. Although the toy box is almost full so if I get another toy I will have to move one into storage.
I got a pretty wooden box that just happened to have a lock from some home decor store (pier 1 maybe?), and keep them there. And inside, I keep the glass or silicone ones inside pouches so nothing touches.