Zotero and Zotfile

Zotero, which is open source software, will manage the references (that you can add automatically with an ISBN or a DOI or by having zotero recognize the pdf’s metadata), you can also have tags, notes, linked documents, etc.. You can also export the library in Bibtex, making bibliographies formatted as you want (you can even create your own custom citation style if you feel like it), integrate it in libreoffice/MS office, etc.. You can also import an existing bibtex file or database from endnote or mendeley.

Zotfile will allow you to define the name formatting you want for your pdfs and the tree structure you want them to be organised in, and automatically rename and refile your pdfs.

(if you’re the kind of nerd that writes in plain text, zotxt will help integrating zotero in your writing)

If you have a LOT of pdfs you might have to import your library in several times (but this painful moment should only happen once).

https://www.zotero.org/

http://zotfile.com/