I had the fun experience of packing up everything last spring when we moved across the state, and I had a lot of the same questions. While I know I don't have nearly the collection that you do Brent (nor the more valuable pieces like Blue Snag), I was trying to be as careful as possible with each figure as well. I'll basically echo what others have said. Basically, each figure got its own ziplock bag, and they were laid side by side. The vintage figures that I have were actually packed up this way, and then put in their own seperate box (a Nike shoe box I think), and then put into a rubbermaid as well. Some of the older POTF2 figures (that I don't really even display anymore) got put in plastic bags, and then stored in the back of my loose POTF2 Falcon. You can hold quite a few in there when stacked up flat, and it was a space saver for me. Again, I didn't have as much to move as you most likely do. After being in the ziplock bags, I also put paper towels between things to help avoid rubbing and/or smashing. The vehicles I broke down as much as possible, removing wings/guns when I could. Those then got wrapped in paper towels or some sort of padding, unless I happened to still have the box to it. I used quite a bit of Wal-Mart/Target bags to cushion between things, along with paper towels and things like that. Everything made the trip just fine, so it seemed to work.
The Unleashed were the biggest pain to pack/ship. I too enjoy them loose, but they also aren't he most compact things in the world to move. Like Dave mentioned, I broke them down as far as they could be, and always took out the weapons (particularly sabers) when I could. Those got packed in a seperate bag/box. The loose figures themselves don't lend themselves to packing well, but we didn't have the space to have them each in individual boxes, so they went in rubbermaids as well. I wrapped each "piece" of them individually in paper towels, using some scotch tape to hold it on around certain areas, then wrapped each of those in Wal-Mart/Target sacks, then I strategically placed them in the rubbermaids, with lots o' padding inbetween and around them.
The little boxed stuff I had was fairly easy. Although more space consuming, you can basically just stack it and be done with it. But, then again, I can't give any advice on that because I really have very little that is still in the boxes, and what I do was fairly easy to pack up. I'd definitely say be the most careful with the Unleashed and valuable stuff. I can see why you are packing it up, I did the same thing when we started showing our house. Having all the shelves up/stuff out definitely makes a room look smaller and I didn't want to worry about missing anything either. I also, like bobafett14 mentioned, labeled my "Star Wars tubs" so I knew to be careful with them, and to have them traveling in a safe place. Best of luck with the packing, moving, house hunting, and house selling though, I hope you guys find exactly what you are looking for.