function fixTables($dbname) {
	// search for all the tables of
	// a db and run repair and optimize
	// note: this can take a lot of time
	// if you have big/many tables.
	$result = mysql_list_tables($dbname) or die(mysql_error());
	while ($row = mysql_fetch_row($result)) {
		mysql_query("REPAIR TABLE $row[0]");
		mysql_query("OPTIMIZE TABLE $row[0]");
	}
}

http://www.barattalo.it/2010/01/25/10-php-usefull-functions-for-mysql-stuff/

Run REPAIR and OPTIMIZE on every table of your MYSQL DB

PHP