Jeepers this has to be one of the kludgiest workarounds I've seen in a while.
While working through some issues on a site I noticed that if I have an HREF pointing to a PDF file it opens fine in IE6, but if I use window.open in the onClick of a button, IE reports that "The website is not available at the moment, try again." Uh huh.
After boatloads of testing to make sure that it worked in every other frigging browser in creation (including IE7) it became clear that I needed a workaround. Here it is: I created a input-less form at the bottom of my page inside of a non-displaying div thus:
<div style="display: none;"><form id="testform" method="GET" target="_blank"></form></div>
note also that the method of the form is GET. In the button I call my own submit function thus:
<input type="button" value="Click here to get it!" onClick="openPDF('/pdfs/thePDF.pdf');">
I handle the function like this: pushing the URL I want to open into the action of the form and submitting it:
<script>
function openPDF(theURL)
{
var target = document.getElementById('testform');
target.action = theURL;
target.submit();
}
</script>
Works like a charm in all browsers, including IE 6

/perk