Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research in your field. Mendeley is a great organization tool for those who have accumulated a large number of PDF files during the research process. Using Mendeley, you can extract metadata from your PDFs which will allow you to index and organize your collection for easy searching and citing. Mendeley is a desktop application but also has an online component so you'll need to download the software onto your computer in order to get started. Mendeley also offers users a mobile option called Mendeley - Reference Manager (Lite) for iPhone, iPod Touch, and iPad.
(from Mendeley's Features page)
Mendeley has both an ONLINE and a DESKTOP side to its application.
The desktop client is a free download and will allow you to store, organize, and manage your PDFs. It also provides an easy way to read and annotate them.
The online site has the same information but does not store the full PDFs (it will give you links to find them in the library); the online site also has extensive social networking features that make it easy to find researchers, groups, and papers you might be interested in and add them to your library or your contacts. Both versions of Mendeley automatically sync with each other, so you never have to worry that a paper you added to the desktop version isn't in the web version (or vice versa).