I've been storing my collection in large and even small rubbermaid bins for years, at one point the accessories were kept with the figures, that was back before I had so many G1 figures. Nowadays I've taken to using the ziplock bag method for storing accessories.
All of the Transformers are kept in their bins by series, so I've got G1/G2/MW together, BW, BM, Armada, Energon, Cybertron, Universe, Classics/Universe 2.0 (what few figures I have from that line.), RID, The Moive and Animated share a bin at the moment due to space issues. Althogh my Movie toys have been on display for weeks now close to two months so yeah.
It also helps to keep them all in one safe place, I store them in the basement in a large pile, and they're always in the exact same place so that when I do rotate the display by series I'll always know which one is where and who goes in what. (Considering half of them are just marked as Transformers and all have the same color bin it helps to be a little anal when it comes to keeping them in the right place.)
It can be a hassle to get at the figures you want when you want them, but then again I'm used to it. I've never had more than one room to myself in any house, the bedroom, so I can't exactly keep everything on display. I've got enough problems with remembering to dust the damn shelves every once in a while.