flpsed is a PostScript annotator. So convert PDF files to PostScript using pdftops and use flpsed.
Scribus is an open-source application for "professional page layout". This means that it is overkill for a PDF viewer if you only annotate occasionally. Hmm. It seems that you have to convert to PostScript here as well (then File -> Import -> Import PS).
These programs can be installed with apt-get.
apt-get install evinceI wonder how hard it would be to merge flpsed and evince.
apt-get install scribus
apt-get install flpsed