mysql_connect('localhost', 'root', 'пароль');

$res = mysql_query('SHOW DATABASES');

while (list($dbname) = mysql_fetch_row($res))
{
        mysql_select_db($dbname);

        $rec = mysql_query('SHOW TABLE STATUS');

        while ($data = mysql_fetch_object($rec))
        if ($data->Engine == 'InnoDB')
        {
                echo 'Processing ', $dbname, '.', $data->Name, ' ... '; flush();

                mysql_query("ALTER TABLE {$data->Name} ENGINE=InnoDB");

                echo "done.n";
        }

        mysql_free_result($rec);
}

mysql_free_result($res);