The only waviness I've really noticed lately is a Legendary Axe manual I have, none of my Japanese games have this problem and all still look pretty great. I can't seem to find my Alien Crush (I'll be heartbroken if I can't find it!) and Keith Courage box but I wonder if it's just a deal with early US game manuals. My Blazing Lazers looks alright, not perfectly crisp but pretty good shape. Trying to flatten the Legendary Axe one under a pile of books right now.
Some of my old Son May CD inserts have collapsed in on themselves, too, so I figure it's just what quality paper you choose.