Update (24/03/2014): The tool will now process not just URL links, but also links that point to other PDF files, and will set all of them to open in a new window.

This tool will easily and quickly convert all of the links in your PDF files, whether they are of the type "Open a weblink" or "Run a JavaScript" to open in a new window.
No need to manually edit hundreds of links just so that your file will remain open when the user clicks a link in it. The tool can batch process entire folders within seconds!

A free demo version of this script is available here.
This version will only convert the first 3 links in the first 3 pages of the first 3 files in the selected folder. Purchase the full version and be able to convert them all!

Important information about viewing PDF files in browsers: The current versions of some browsers (Firefox, Chrome, Safari) contain their own PDF viewer plugins, which are often not very compliant with the full PDF standards and usually have problems with executing JavaScript code.
As a result, if you're using one of these browsers to view the files processed by this tool you might encounter some problems. To solve them read this page on how to set up the Adobe plugin as the default PDF handler in your browser:
http://helpx.adobe.com/acrobat/using/display-pdf-browser-acrobat-xi.html

Here's how it looks like:

(click to enlarge)

NOTE: This application does NOT require you to have Acrobat or even Reader, and it will run on both Windows and Macintosh computers. You do need to have Java installed, though.