I was searching for tools that allow easy commenting and highlighting of PDF files.
Xournal is good but it doesn’t parse the pdf file. xournal creates a layer on top of the pdf, where the user can draw or write annotations. it also doesn’t allow to write comments that can be hidden/expanded. u can get xournal through ubuntu software center
the linux version doesn’t offer annotations or highlighting. you need to install a windows version with wine. versions that worked
Update: Acrobat reader 9, which you can get for free, has the functionality to comment, highlight and draw.