I'm assuming you are opening these from an HTML page. If you use a target="_blank" in the href (to open the PDF) it should work, you might have issue with some popup blockers.
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If you're referring to links inside a PDF file, then yes, using app.launchURL in a script is the only way of doing it.
And if you want to do it in batch to all of the links in your file(s) then you will need to use a plugin or a stand-alone tool, like this one I've developed: Custom-made Adobe Scripts: Convert all links in a PDF to Open In New Window
Although Acrobat doesn't have a link code that will force a Weblink to open in a new window, here's how you can make it happen without worrying whether your users have selected "Open Cross-Doc Links In Same Window."
Rather than linking directly to the URL you want to open, create a link to an HTML document that contains no text. The HTML document immediately opens a new window itself, using HTML code rather than Acrobat's syntax, and opens the desired URL in that window.
The Acrobat Weblink will be a normal link to an HTML page that has nothing in its body and includes the following line in its head:
< META HTTP-EQUIV="Refresh" CONTENT="x; URL=zzz" >
For x, substitute the number of seconds that should elapse before the new link opens (in this case, probably zero).
And for zzz, substitute the URL that should open in the new window.
Thanks for the help guys.
With the inconsistent behaviour of PDF viewers in all the browsers, I think we will be looking at getting people to download the PDF and use it through Adobe Reader and not encouraging the use of it through the browsers at all. We simply can not afford to have something change and 16,000 links go silent.