Updated
You made PHP tags within echo
. That's pretty wrong!
As I understand OP:
$text = htmlentities('<?php echo \'<pre><p align="center"><iframe src="aufgaben/"+cookieValue+"/"+cookieValue+".html" width="322" height="497" frameborder="0"></iframe></p></pre>\'; ?>');
echo "<script type='text/javascript'>
iframe0document.getElementById('jform_articletext').value = ".$text.";
</script>";
You need htmlentities
function to encode characters to their html equivalents and print out php tags az plain text.