Nice suggestion! I'll add that in as a user configurable option for the next release. It's a really easy thing to do on your own installation, though. Simply add a target parameter to any links you want to open a new window....
For instance, you could modify a line in generate_category_html() to be:

$html .= qq{<A HREF="$PMURLINDEX?node_id=$nodeid" TARGET="pm">$title</
+A>};
[download]

Thanks for the feedback.

-Blake