Reference-management tools, also called citation managers, perform a handful of related functions: searching the literature; storing and organizing PDFs of papers and supplementary materials; generating bibliographies; and fostering collaboration. Often they also incorporate reading and annotation functions (taking notes, highlighting, tagging, etc). While there are dozens of options, here are some of the most popular:

Zotero—A free, easy-to-use tool to help you collect, organize, cite, and share research.

Mendeley—A free reference manager and PDF reader.

Papers—This application aims to improve the way you find, access, organize, read, share, and cite scholarly literature.

Endnote—A tool for managing bibliographies, citations and references on the Windows and Macintosh desktop.