A quick FYI: A while ago there was a thread on this list discussing the possibility of adding annotations to a PDF [1] using Free software, mainly as a way in which an editor can add comments on a manuscript. It seemed that there were three options: 1) purchasing Adobe Acrobat Standard; 2) waiting for the poppler library and associated tools (KDE's okular and GNOME's evince) to add this functionality; 3) using a Windows program.
It seems that there's now another possibility which is a PostScript annotator "flpsed" [2] which has the ability to convert to/from PDF. This was mentioned in the comments to a recent Linux Journal article on working with PDFs in GNU/Linux [3]. 1. http://www.mail-archive.com/lyx-users@lists.lyx.org/msg54320.html 2. http://www.ecademix.com/JohannesHofmann/flpsed.html 3. http://www.linuxjournal.com/node/1000235