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 optimization for every table in the database and/or server install, or is this something you'd have to script up yourself?
You can use mysqlcheck
to do this at the command line.
One database:
mysqlcheck -o <db_schema_name>
All databases:
mysqlcheck -o --all-databases