I actually only remember one game doing this, XIII, a cel-shaded shooter, seriously, you'd think they'd spent more time protecting the game than developing.
If i recall correctly parts of the copy protection were everywhere, they were in executables, in textures, models, maps, etc.
So basically they had taken care of the copy protection, but the copy protection were still there due to being implemented in various game assets, heck you'd get to a point in the level and it would say something like "To get this key, you should purchase the full game", the key was of course a prerequisite for some goal in the map that allowed you to progress.
I don't even think it got cracked, there was simply so much copy protection that they couldn't be bothered in the end, every time they fixed something like the key, then it was suddenly another thing, and so on, and so on.