If money allows me to, I'm definitely going to get plastic protectors for the boxes I have. I've heard both good and bad, but personally I feel that as long as you're getting acid-free plastics, you're in good shape.
And since you mentioned making your own boxes...
I've made close to 150 NES box reproductions out of thick stock (100# Matte Cover) and they came out great. This was done with images sourced from TCP and adjusted to fit a template I put together:

(original on left, repro on right)
The stock isn't quite as thick and isn't really "cardboard" (or "kraft" paper as it's called in the paper industry), but it's fairly solid and would look great in a plastic protector.
I did this with the black boxes and they look pretty nice:

They're just a *tiny* bit smaller than the actual boxes depth-wise, but it's barely noticeable. This picture was taken right after I cut and folded, so the flaps stick up a bit and haven't been folded down enough.
I've done Game Boy, SNES, and N64 boxes too, but I haven't tried putting them together yet.