If you're a member of a lot of groups or have a lot of pending invites they probably generate a fair few messages in your facebook inbox that you don't really care about. The messages you DO care about tend to be the ones from an individual to you. Those are the ones you want to be notified about by email and not the rest.
At the moment facebook doesn't give you the option to be notified about one type of message but not the other. That means your email inbox can quickly fill up with facebook notifications that don't interest you.
One answer is to use email filters and in this post I'll explain how to set that up.