At its most basic level, Mendeley is a citation management tool, but it can also help with other aspects of research, such as organizing PDFs of research papers, including annotations and highlights, inserting bibliographies and citations into a word processor, and sharing research with collaborators (links to libgude).
Zotero is a free citation management software plug in for Mozilla Firefox, Chrome, and Safari. It enables users to collect, manage, and cite research from all types of sources. It is easy to use, lives in your web browser where you do your work, and it is free! Zotero allows you to attach pdfs, notes, images and screenshots to your citations, to organize them into collections for different projects, and to create bibliographies using Word or OpenOffice (links to libguide).
EndNote is similar to Refworks and Zotero, but it allows you to produce bibliographies in a greater number of citation styles and allows greater customization. It is particularly popular in the sciences (link leads to libguide).
CiteULike lets you easily store references you find online, discover new articles and resources, has automated article recommendations, share references with your peers, find out who's reading what you're reading, and store and search your PDFs.
Collect, write & discuss scientific literature with experts in biology and medicine. This new citation manager allows you to organize your citations, write faster with a word plugin, and collaborate with others through projects.