Tayfun Sonmez will be offering an undergraduate course on market design at Boston College: Advanced Microeconomic Theory (T Th 13:30 - 14:45 AM).
There's no web site, but the course focuses on various aspects of matching, including some of Tayfun's latest work.
Susan Athey will be offering an undergrad course on market design at Harvard:
Economics 1056: Market Design Harvard College/GSAS: 69207 Fall 2011-2012 Location: Sever Hall 106, Meeting Time: Tu., Th., 2:30-4
Ben Edelman and Peter Coles will be offering an MBA course at HBS,
Peter Coles and I will be giving a graduate course on market design at Harvard:
Economics 2056a: Market Design Harvard College/GSAS: 3634, Fall 2011-2012, Location: Littauer Center M-16, Meeting Time: F., 9-12
And next semester, Parag Pathak will be offering an undergrad course in market design at MIT.
Update: and Sven Seuken points out that David Parkes at Harvard is offering "Economics and Computation" in Computer Science this Fall. It will touch on a couple of market design topics: http://www.seas.harvard.edu/courses/cs186/