Each researcher spends quality time managing the literature that they have collected in the form of papers and PDF’s. However, the collection of PDF continues to grow and there are very little in the form of tools that help manage it. There are three(3) great open source tools that work wonderfully to manage the collection of PDF’s.
I,librarian: This is a complete collection of web server and PHP based programs that manage the database of PDF’s in a SQLite interface. This has bee around for quite some time and has a great interface. The negative is that it requires the installation of the webserver that will manage the database and serve it over a web page. It serves most purposes and the ability to see the source code is very useful. You can also try some of its work by looking and trying out a large database as one operated by Canadian Council on Animal Care. Interestingly they also have a touch screen friendly interface that enables reference lookup through a mobile device. They also make installation easier for windows and Linux users.
http://www.bioinformatics.org/librarian/
Jabref: This has been created in Java so is relatively platform independent. This is also better oriented towards LaTeX and BIBTeX files but will also work equally well with PDF.
Refbase: This is a another great database that has a great interface, good search capability and also an ability to gather the RSS feed. This is also capable of reading a wide variety of documents including Microsoft Word and Excel files. They can manage to create direct download links as well as a convenient way to upload files. What distinguishes this database is their ability to use MySQL and that makes them very rugged and search optimized. This may be more linux friendly and so will require a more knowledge of the operating system to install.
refbase: http://www.refbase.net