I don't really understand your problem. In Windows, MySQL puts the data files in a directory named data. It creates a sub-directory inside data with the same name as the database name. Every table from the database is dvided into three files, with extensions .frm, .MYD and .MYI
You can get the databases name from a MySQL server by using <B>SHOW DATABASES</B>, and the tables from a database by <B>SHOW TABLES FROM database_name</B>
I suppose that in Linux, must be the same. You can make a script that reads the size of each of the files that make the tables of each of the databases in the server. Then, it connects to another server that will contain the data of the sizes of the files from ALL OF THE SERVERS. Sort of a master server thing.
This way you can cron the script daily and know how much space is the db taking up, knowing if it needs some cleaning.
Hope this helps
fLIPIS