## CODE
 
mysql -u<username> -p<password> <DATABASE name> -e "OPTIMIZE TABLE `table1`, `table2`, `etc`;"
 
## NOTE: Something LIKE this may help. Dan W  made this script FROM his own
## knowledge, AND a little bit OF research ON Google. This script can ONLY 
## OPTIMIZE one DATABASE. IF you need TO OPTIMIZE more than one, you will 
## have TO ADD a few more LINES OF code IN there.
 
## CODE
 
<?php
 
$server = 'localhost';
$username = 'mysql_username';
$password = 'mysql_password';
$database = 'mysql_database_name';
 
### connects TO the DATABASE, OR dies WITH error
$connection = mysql_connect($server,$username,$password);
IF (!$connection)
{
  die( mysql_error() );
}
 
### selects the db OF choice, OR dies WITH error
$db_selection = mysql_select_db($database, $connection);
IF (!$db_selection)
{
  die( mysql_error() );
}
 
### selects ALL TABLES IN the db OF choice, OR dies WITH error
$alltables = mysql_query("SHOW TABLES") OR die ( mysql_error() );
 
### loops through ALL OF the TABLES AND optimizes each, OR dies WITH error
while ( $table = mysql_fetch_array($alltables) )
{
  mysql_query("OPTIMIZE TABLE `".$table."`") OR die( mysql_error() );
}
 
### closes the mysql connection
mysql_close($connection);
 
?>
 
## Be sure TO edit the VARIABLES at the top TO the VALUES that are 
## appropriate FOR you. WHEN you GO TO run your cron job, again just 
## do "php /full/path/to/script.php" AND since optimizing TABLES may 
## LOCK down your DB FOR a SECOND, run the script at a TIME WHEN you 
## don't expect traffic.