We keep ours in the same thing. A couple are bagged, but after living through the 90s comic speculation boom and bust I'm inclined to be pretty nonchalant with how I store things now.
We also don't have many floppys anymore, so it's not taking up that much space. If I had a ton I'd probably get some standard longboxes and make space under a bed or something.
I do need to organize my manga better though. At least I've stopped buying Japanese volumes I can't read.