MySQL has an OPTIMIZE TABLE command which can be used to reclaim unused space in a MySQL install. Is there a way (built-in command or common stored procedure) to run this o
The MySQL Administrator (part of the MySQL GUI Tools) can do that for you on a database level.
Just select your schema and press the Maintenance button in the bottom right corner.
Since the GUI Tools have reached End-of-life status they are hard to find on the mysql page. Found them via Google: http://dev.mysql.com/downloads/gui-tools/5.0.html
I don't know if the new MySQL Workbench can do that, too.
And you can use the mysqlcheck command line tool which should be able to do that, too.