If a toy doesn't come with a pouch, I hand sew one for it (and trust me, I've made a BUNCH!). Some glass pieces do come with pouches (SSA Glass I believe)... they're not the most protective, but I figure I don't travel with the toys, so if I'm just setting them in a drawer (where they're not moving around much), I'll leave them in those bags. For glass pieces that didn't come with a pouch, I sew pouches from old hooded sweatshirts, instead of the thinner material I use for non-glass toys. It works great!
As for storing them (and all my other toys), I bought a simple, plastic drawer tower from Wal-Mart. It was a five drawer one (with two thin drawers on top, three biggers ones on the bottom). I use it as a night stand next to my bed, though I had to take one of the top thin drawers off because the whole thing was too high to sit next to my bed. The whole thing works great though... top drawer acts as a regular night stand drawer with night stand stuff (wallet, lipbalm, random junk, my most used clit toy, etc)... the rest of my toys are divided between the bottom drawers (anal, clit, G-spot, glass, etc). It works out great, though the drawers are clear plastic... but since all my handmade pouches are black, you can't see a thing