This is including the clerks picked by the late Chief Justice, William Rehnquist, even though their fate is unknown (at least to me)--but the fact that the Chief Justice picked these clerks reflects well on them and their institutions.
Here are the schools represented among the 2005 term clerks:
1. Harvard University (10)
2. Yale University (6)
3. Stanford University (4)
4. University of Chicago (3)
There are two each from George Washington University, University of Virginia, and Columbia University. There is one each from Vanderbilt University, Oxford University (who did postgraduate law study at Georgetown), University of Michigan, University of Georgia, and University of California at Berkeley.
UPDATE: Thanks to my colleague Keith Whittington who points out that C.J. Roberts hired all the Rehnquist clerks, as well as bringing along some of his own (not counted here, since they weren't hired in the more competitive Supreme Court market).