I have been using Emacs org-mode for about 3 months now, loving every bit of it so far.   One of  the killer feartures is the capture from external applications (e.g. Web Browsers).  After some struggling, I can successfully capture from Firefox and Chrome, but I am still having trouble with Adobe Acrobat Reader.  After adapting XDG-open, I can only capture the PDF file link (not the selection though), with two Firefox Windows popping up and an error message.  I have documented this in my blogs (http://tech.memoryimprintstudio.com/?p=160).