blind me just now discovered the fact that xournal has ways to annotate PDFs.
that is uber useful feature -- THANKS for it a lot

right away though I asked myself -- how can I find annotations in my 200pages phd thesis without looking through all the pages... and found no way to accomplish the mission. Suggestion by Max is one way to treat the problem and it would fit me as well: if there are bookmarks to the pages with annotations -- I am happy ;) another useful addition might be right within xournal: browsing of pages with annotations (prev/next page with annotation or list of pages with annotations with ability to jump to a corresponding page). Adding comments to a group of annotations would be even better but I don't see that as an easy addition to xournal atm.

To summarize: having bookmarks in the exported PDF would be really useful!
Thanks in advance and keep on great work