Boxes for iPhones and iPads are used legitimately to sell used items for a higher price. If you're going to trade in an iPhone to Amazon, you'll get a higher value if it has the original packaging as opposed to just the phone itself. If you're going to sell an item on the open market (e.g., eBay, craigslist), brokers and resellers often times prefer to have the complete package, so when they resell them overseas, they bet a higher return. Finally, if you bought a device to give to someone as a gift, it las much nicer to receive it in the package. This is not intended or scammers to package with loose paper and dupe someone into thinking it's the actual device itself.
Apple and eBay have an agreement to not allow auctions for Apple items that are not generally sold as standalone products. In the past, I've sold boxes very clearly listed for the reasons above.
Long story short, it's a legitimate reason that many people do. I'll likely recycle them, as they're taking up too much space.
If someone here wants them, they can have them for the cost of shipping (I don't care to make money off of them at this point; consider it my first Karma on this forum).