I shipped a couple out and I found the best way to ship them is to pack the system in its original box and pack that box in a large computer box (i.e. a box that a desktop shipped in). These usually have nice foam brackets in them that will support the ps3 box nicely and usually they are around the same size. You might be able to score some of these at schools or offices or might have one in your attic or basement if you bought a computer at some point. Once you pack it I would fill the entire box with additional styrofoam peanuts to pack it completely. I would wrap the PS3 box in bubble wrap first as well. Also it sounds redundant, but I would write "Fragile" with a sharpie on all sides of the box.
As for shipping, unfortunately it is going to cost a good bit to ship it. I recommend using UPS Ground and buying the extra insurance. There is no way I would ship something like this via the post office, and I would not use media mail as was suggested as a PS3 definitely does not qualify. I know some people claim they can dupe the system and ship anything media mail, but why risk it on a high value item like this? I also would not want to deal with the post office on an insurance claim on an item like this. Don't get me wrong, I'll use Priority Flat rate boxes/mailers for $50/60 games, but I wouldn't trust them for a high value item like a PS3.
If you are going the ebay route, I'd just use the calculators that ebay provides in your auction and pass the shipping cost straight through to the buyer. Or just use a flat rate shipping cost of $30. I think that is around what it cost me to ship UPS GROUND, which included like $600 in insurance. Like I said, its not the cheapest way to go, but if you are selling a gunmetal PS3, your target customer isn't the average CAG looking to get a PS3 for $200 + $10 shipping.