Selecting this option from the Database Navigator will open a window and automatically perform an "ANALYZE TABLE" command on all MyISAM and BDB tables (the command isn't supported for other table types).
Analyze and Optimize Tables window
There are two buttons at the top of the screen - the left one will perform the ANALYZE command for all tables, this already is automatically done for all tables when the screen gets openened.
The right button will perform an OPTIMIZE TABLE command for the selected tables.
See the MySQL documentation for more information on these commands.