My current method of Joe storage is vehicles in bins, parts removed, bagged, labeled, and laid on top of the vehicles just under the lid when the bin's full. For the figures (25th style), they're all stuffed in one Ziploc with their accessories in another, and they have their own bin. One day I'm going to bag them with their accessories individually, but that will take a lot of time...and Ziploc stock should take a big jump when I do!
I know your pain, LJ. You guys have seen just a fraction of my collection in my reviews, and I live in a freaking one bedroom apartment! Thank GOD it has an extra walk-in closet (one closet for clothes, one for Joes

). One day I'll have to take a pic of my closet just to show how stuffed full it is.
LJ, it would take even longer, but I'll tell you my method of Transformers storage too. I've got around 100+ Transformers, and considering that especially the early ones (with real metal) can get chipped up, I wrap them individually in bubble wrap, label them, put their accessories in a Ziploc snack bag, tape THAT to the bubblewrapped Transformer, and then carefully put them in a bin. Time consuming and expensive with the bubble wrap, but a LOT better than chipped Transformers.