I've gotten pretty good at sorting/packing stuff, just because I have always had hundreds of thousands of items.
I still love the battery boxes for temporary storage of media. Easy to stack and transport. Obviously I wouldn't use them for soft boxed or highly collectable stuff, but they are an easy way to move a DVD shelf of stuff while keeping them in order if you are moving the stuff yourself.
Priority flat rate boxes work well for guides, comics, books, etc. You can order them free from the USPS website and drop them off if you do not intend to use them. My PO is happy to get some of the oddball boxes b/c they are not allowed to order them.
As far as Saturn/Sega CD games go, I was working on what to do with them yesterday. I decided to line a dresser drawer and set them in there since I am scared I will somehow destroy them if they are in a box on a shelf.