Yeah, about search:

    $ pdfgrep -r -i -n -H "your mom" ~/PDFArchives/

Very effective, very fast, very private. Bonus points if the PDF filename itself is derived from a well formulated <title> tag, such that you can just use “ls” ..

You could combine it with existing products like DevonThink that are meant for researchers organizing documents and provide tagging, semantic search, similarity graphs, and so on.