Classic bibliographic citation systems have come a long way and are much more interactive and responsive. They help keep track of secondary literature by working directly with commercial databases (Proquest, Ebsco, etc.), single web pages, image resources, and more. Many of the products out there also have plugins to work in tandem with word processing software.
RefWorks is a web-based citation management software that gathers, manages, and stores citations, generates bibliographies to share with colleagues (using RefShare), and, works with or in replacement of EndNote or Reference Manager. People like RefWorks because the system is web-based making your database accessible from anywhere, the library pays the subscription fee so it's free to users, it automatically updates output styles so you don't have to install update files, and it is Mac and Windows compatible. Have a look at the RefWorks Fundamentals video tutorial or look at the Library's RefWorks guide for helpful tips and info on getting started.
Mendeley is a freely available application that you can install on your desktop or use on the web. You can sync your library across multiple computers, on the web, and on iPhone/iPad. Probably the biggest strength of Mendeley is its management of PDFs; you can read, annotate, import and organize PDFs on your hard drive or other citation management software. It also enables you to collaborate with colleagues, sharing share papers, notes and annotations. For help getting started finding and managing citations, watch the Mendeley Video Tutorialsor read the Getting Started Guide (also available from within the Desktop installation) or the Mendeley Help Guides.
Zotero saves, collects, manages, cites, and shares citations and other resources. Zotero is available either as a Firefox extension or as standalone software that works with Chrome and Safari browsers. It works right in your browser, making it easy to save citations while you search. You may attach PDFs, notes and images to your citations, organize them into collections for different projects, and create bibliographies. For a great overview of Zotero, check out this guide. Best of all, it's free.
Bookends is a full-featured bibliography, reference, and information management system designed specifically for the Mac operating system, e.g., Mac OS X 10.4 or later. The sync feature makes your database portable, the reference linking allows you to make notes and show connections, just like old fashion notecards, and it works with several different word processors. Bookends is unicode-savvy, so you can mix Roman (English, French, German, etc.) and non-Roman (Japanese, Greek, Hebrew, etc.) characters. Check out this short video for more information. Bookends is not free nor is it supported by OIT.