There are a number of rules. One thing I know is that Muslims believe a Quran should never be destroyed, as it is considered the literal word of Allah. I knew a Christian author once who published her book on a page with watermarks of the Qur'an behind the Bible verse. This meant the Muslims could not throw the book away!
You also have to handle it with your right hand, as the left hand is the one you are supposed to use to clean yourself.
Also, you cannot lay any other books on top if it. I also think it isn't supposed to hit the floor, but I am not sure about that one.