I use Zotero as a PDF file manager, appreciating the search functionality. However, as the database grows larger, so does the fear that one day, the connection between database and the files will be broken. I know that in theory, this fear is unjust, but practice often proves otherwise (think about managing mp3's and pictures).

Therefore it would be great to have all metadata in the database, with an option to embed it in those files that can hold the metadata. If one day you're left with just a back up of the pdf folder, or part of it you happened to send to someone by email, importing all (PDF) documents would then be a breeze.