Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.

Aigaion Reference Management System - Aigaion is a bibliography management system that seems to be the perfect tool for managing your bibliography and references.

Paperpile - Clean and simple and reference management for the web. Sync your PDFs to Google Drive and cite your papers in Google Docs.

BibBase - BibBase.org is an easy way to set up and maintain a scientific publications page.

JabRef - Graphical Java application for managing bibtex (. bib) databases.‎JabRef · ‎JabRef Help · ‎JabRef | Blog · ‎OpenOffice/LibreOffice .

I Librarian - I Librarian is an online tool that comes with a great way to handle and manage your PDF paper and office documents.