Zotero is a Citation Management tool highly recommended for students and faculty that regularly download and use research materials. It allows users to easily import PDF's into a personal research collection while preserving bibliographic metadata. Once the research materials have been downloaded, they can be organized locally on your harddrive through the Zotero interface. A special file hierarchy used only for your research collection can be customized to suit your needs! Documents can also be tagged according to the project, semester, or class they relate to. Finally, Zotero integrates with your word processor of choice, allowing you to automatically generate citations for the materials in your collection while in the process of writing your next paper or manuscript.
If you would like to begin using this tool, the easiest way is to follow this tutorial I created. Using animations and clear instructions it will take you from installation to mastery of the four key functions: collecting, organizing, citing, and sharing.