Supposedly RDF caused poor performance and it was replaced by https://community.kde.org/Baloo which uses sqlite+xapian. The nepomuk ontologies live on in the Digital.ME research project, which seems to be a research prototype in Java for a "cross-device social semantic desktop", but there's no active dev community.

http://www.semanticdesktop.org/ontologies/

http://www.dime-project.eu/ & http://dime-project.github.io/

Edit: recent article on Baloo: http://xmodulo.com/2014/07/kde-semantic-desktop-nepomuk-balo...

Maybe the semantic desktop should be a semantic server? Run it on a dedicated PC that also serves as NAS. It would be a relatively small price to pay for a secure pkb with cross-platform clients.