Mendeley is a program that sorts and organizes PDFs, allowing you to easily keep track of papers you've read. Mendeley allows you to highlight and take notes on your PDFs, and all of your notes (as well as the full text of PDFs) are searchable... so you can quit saying "I read a paper somewhere..." and find exactly where it is.
Mendeley easily exports bibliographies to Word or BibTeX, so making your works cited page is simple. Mendeley also features a sync to the internet, so your work is backed up, and has a smartphone app so you can read papers on the go.
Mendeley combines features of programs like EndNote, Papers, Sente, and Zotero in one convient and easy to use piece of software. Plus, Mendeley is free
(for now, they hint it might not always be), so go ahead and check it out!
Update: Mendeley will always have a free version (See Response from Mendeley below)