If you want to call json_encode there, you need to do this.
$jscode = json_encode($message).';return false';
You don't even need json_encode for this. You can put this there:
$message = 'centeredPopup(this.href,"myWindow","500","300","yes")';
$jscode = $message.';return false';
$list .= '<p> <a href="http://www.example.com/something.php?id=' . $id . '" onclick="' .htmlspecialchars($jscode) . '" >' . $name . '</a></p><br>';