Anki - Secretly powerful multimedia flash card download built for syncing between your computer, online or iPhones and similar device.
CoboCards - This well-designed, easy to navigate web application focuses on collaboration perhaps more than any other site on this list.
Cramberry - Good online application for vocabulary and other things you could fit in just one line of text (that's the limit). Works on your iPod Touch/iPhone as well.
FlashcardExchange - This site has a large web-based library of ready-to-study flash cards, and a free account allows you to create and study online. More advanced options (like sharing or printing your cards) required a paid membership.
Flashcard Machine - Collaborative, multimedia web-based application great for teachers; they can set up a stack of cards that can be accessed without registering for an account on the site.
Genius - Simple, no frills text-based flash cards. [Mac only]
Memorize.com - Simple, web-based virtual flash cards for yourself or collaboration with others. Setup email reminders to make sure you study, and then do so in a variety of ways.
Memorizer - Forget about fancy user interfaces. This download is as utilitarian as it gets, but it has one key feature: Your simple, text-based flash cards popup randomly while you're using your computer for other things, so you're always studying (sort of). [Windows only]
Mnemosyne - Perhaps the most interesting software on the list, when you use Mnemosyne, you can contribute to research on human memory and how "flash card" style repetition and studying works.
Pauker - This free, open-source option is simple and text-only. It works on all platforms, but you must have Java installed.
Quizlet - More than just flash cards, Quizlet is a web-based application that allows you to both create study materials and quiz yourself (or others) on the materials. It's also a good option for those that want to share via social networks like Facebook.
Study Stack - This website's best feature is its well established collection of already created study guides. Or maybe it's playing hangman or a crossword puzzle with your flash cards.
Teach2000 - Powerful, option-rich download that has a handy USB drive versions, which is great for those of us that can't install programs on our school computers. [Windows]
Did I leave your favorite free application off the list? Do you have any positive or negative reviews of any of these? Share your thoughts in the comments.