The 25 Top Censored Stories of 2009 according to Sonoma State University's excellent Project Censored are listed after the fold.
There is also a poll: please vote for the story you think was the most important of them all.
I agree so much with this Walter Cronkite quote: "Project censored is one of the organizations that we should listen to, to be assured that our newspapers and our broadcast outlets are practicing thorough and ethical journalism."