<?php

$aDB = array('db_name_1', 'db_name_2', 'db_name_3'); // Массив имен баз данных.

function Connect() { // Функция подключения к MySQL.
    $link = mysql_connect('localhost', 'root', 'pass') or die('mysql_connect');
    return $link;
}

$link = Connect();

foreach ($aDB as $db_name) {
    $data = array();
    $sql = 'SHOW TABLE STATUS FROM `' . $db_name . '` WHERE `Data_free` > 0';
    $result = mysql_query($sql);
    if (mysql_num_rows($result) > 0) {
        while ($row = mysql_fetch_assoc($result)) {
            $data[] = '`' . $db_name . '`.`' . $row['Name'] . '`';
        }
        mysql_free_result($result);
    } else continue;

    $sql = 'OPTIMIZE TABLE ' . implode(',', $data);
    mysql_query($sql);
}

?>