I donated to the following charities and organizations in the past year (although I really meant to get this post out before the end of 2009):
UNICEF, to support relief operations following the earthquake in Haiti.
The Free Software Foundation, which has a simple but lofty goal: to ensure that the computers we use and carry around with us every day are actually accountable to us. Their public awareness efforts are invaluable, but if they did nothing but maintain the GNU operating system (including, ahem, Emacs), I would still be thankful beyond measure.
Wikipedia, for being one of the things that makes the web so wonderful.
Creative Commons, for showing that we can do better than "All rights reserved."
MIT Open CourseWare, for disseminating knowledge. OCW relies on donations to keep the lights on and to fund digitization of more classes.
My local branch of Feeding America (aka Second Harvest Food Bank). There is something depraved about hunger in the midst of plenty, and so close to home.
Amnesty International, that everyone may have the basic human dignities that you and I enjoy.