Hmm, I think all of my big box games came with the foam to begin with, and even if any were missing, I doubt I'd bother to replace them. As for plastic bags, while the idea of keeping dust from building on top of my games is nice, it eliminates the convenience of just popping the cases open. I think plastic baggies make more sense for regular jewel case games since then you can at least keep the obi against the spine if you want, plus jewel cases sometimes wear out and don't hold shut well anymore.
If I could replace anything, I'd go with the big boxes themselves. I don't know if it's just me, but it seems like the plastic covers often aren't attached to the box well. Far too many of my games have the seam attaching them partially torn, with a corner of the cover flapping loose.