Make MySQL database size a part of Website Quota
There is already a feature request (http://bugtracker.ispconfig.org/index.php?do=details&task_id=1105&project=3&order=votes&sort=desc) to show the size of MySQL-tables, but I think this is not enough.
The size of each database should be added to website quota. E.g. Somebody has 50MB website quota. At the moment it doesnt matter how big the databses are. As a result the customer can use a lot more than 50MB if the databases are really big, because the databases are not counting!
Make it that way: The costumer has 50MB website quota. He uses 40MB for website files (html,..), then there are 10MB left for databases. If the 50MB are reached it should be blocked.