Hi! I manage my research reference papers with Org-mode similar to .
Since I got an Android tablet I pretty much enjoy an automatism to get the actual text of annotations and highlighting back to Org-mode as well. Take a look to  where I put an example shell script with a short documentation. 1. http://tincman.wordpress.com/2011/01/04/research-paper-management-with-emacs-org-mode-and-reftex/ 2. https://github.com/novoid/extract_pdf_annotations_to_orgmode -- Karl Voit