A quick script to do so:

<?php
mysql_connect('localhost','root','YOURPASSWORD');
$alldbs=mysql_query("SHOW DATABASES");
while ($dbs = mysql_fetch_assoc($alldbs)) {
	foreach($dbs as $db_name){
		if($db_name=='information_schema' || $db_name=='mysql')continue;
		mysql_select_db($db_name);
		echo '<strong>database: '.$db_name.'</strong><br />';
		$alltables = mysql_query("SHOW TABLES");
		while ($table = mysql_fetch_assoc($alltables)) {
			foreach ($table as $db => $tablename) {
				echo 'optimising '.$tablename.'<br />';
				mysql_query("OPTIMIZE TABLE `".$tablename."`") or die(mysql_error());
			}
		}
	}
}

Based on this original script for optimising all tables in a specific database.