Here are two journalism programs that are doing it right: one on the undergraduate level at the University of Texas-Austin, the other on the graduate level at American University here in Washington, D.C.
Also, here are two websites that intrigue me: the Northern Virginia Writing Project at George Mason University, and WiredAcademic.com, the brainchild of two terrific young men I first met at the Neuharth School of Journalism a while back: Paul Glader and Biagio Arobba.