Unless you find boxes that fit each different sized book snuggly it wouldn't really help. Your books would just bounce around inside the protector, causing more damage then just sitting on a shelf normally. I'd go with bags. Clear bags will protect them from dust, light scratches, and stains.
You can always use cardboard triangles at the corners to prevent them from denting. Vacume sealing is an option too if you never want to get into your books again.
But if you ask me, you'll spend more money trying to protect your books then they're valued at (unless you have some rare books). Bags are probably the most economical and functional way to go.
