I use open fabric bins from The Container Store, like these:
http://www.containerstore.com/shop/...93&green=93C9EBDE-D8E3-5A11-9D7C-01AF775F9373
I have them all arranged on a low shelf behind doors, so it's easy for me to reach them.
Then I put each bag in a dust cover (either the one it came with, or a pillow case). I don't stuff the bags, but I make sure that before I put a bag away it is COMPLETELY empty and fresh. I stack a few bags on top of each other, but not too many, because I don't want them to get too smooshed.
BTW, I don't know if this is the right way to do it... I'm new to the world of designer bags, and I don't have anything incredibly expensive (like a Birkin). But I do have some nice bags, and I plan to add to my collection.
I'd love to know if I'm making a mistake stacking my bags, so if someone could give me some feedback I'd really appreciate it. I am learning SO much from The Purse Forum!