This feature will optimize and repair all MyISAM tables of your Mysql database. With the flow of inserts and deletes, the Mysql tables performance can drop. Regularly optimize and repair Mysql tables allow to rebuild the indexes and limit the disk space used by Mysql on the server. It's impossible to compute a InnoDB table fragmentation, this is why those tables are not included on optimization process.
Database administrators recommend a MONTHLY optimization of MyISAM tables.