There is now a debian package available to install jpdfbookmarks. It has been created by Slavko http://debs.slavino.sk and it is surely the best way to install the program on linux debian.
The repositories to add are:
deb http://debs.slavino.sk testing main non-free
deb-src http://debs.slavino.sk testing main non-free
the signature file is at http://debs.slavino.sk/repo.asc.
Thank you very much Slavko and I hope others will follow your example and create packages for other distributions.