Zotero
Zotero is an easy-to-use yet powerful research tool that helps you gather, organize, and analyze sources (citations, full texts, web pages, images, and other objects), and lets you share the results of your research in a variety of ways. Zotero is an add-on to the Firefox browser. The Zotero Support web page includes tips and information on installation and use.
Mendeley
Mendeley is a free online service that allows you to index and organize your PDF documents, collaborate with fellow researchers and share information via shared and public collections, and discover new research through the Mendeley academic social network. In addition, you can create reference lists and bibliographies in Word (Windows only) or OpenOffice (all platforms).
RefWorks
RefWorks is cloud-based and allows for easy collaboration. Access to RefWorks is provided by the UCB Library to UCB students, staff, and faculty. Alumni can keep their RefWorks access as long as UCB continues to subscribe. Use RefWorks to store/organize citations, store PDFs, and work with Word or Google Docs to cite your documents.
EndNote
EndNote automates the creation of bibliographies. Save hours of typing by simply selecting the publication or style by name and generating a perfectly formatted document. EndNote currently offers over 4500 styles. EndNote allows you to store PDFs and other files in your database. EndNote Online offers a free version.
My NCBI
Use My NCBI to permanently save citations. Citations from PubMed can be easily added to a My NCBI Collection; you can also add citations from PubMed or elsewhere to My Bibliography in My NCBI.
My NCBI Help Manual