Application for manage and sync PDF collection Unfortunately is not possible synch the PDFs files  using iBook, so i'm looking for an alternative.
I have a huge collection of PDF file and i work with different computers.

I'm looking for an application that can takes care of all my PDFs and generate an archive that can be put on Dropbox / iCloud Drive.

Sometink like Calibre but possibly with a better UX. It shouldn't be necessarely free.

Thanks.
Try one of these for PDF management:

http://reinventedsoftware.com/together/
This works with iCloud to access your library on multiple devices

http://www.ironicsoftware.com/yep/

You can also attach PDF's to notes in evernote.com