I've produced these lists before, using the reputational data from U.S. News surveys.  This year, they did new surveys of humanities and social science fields (as well as the professional fields).  In the past, I gave more weight to breadth of strength; this time I've used a weighting system that gives more weight to depth (i.e., really top programs).  We looked at sixteen areas:  Business, Law Medicine (Research), Biology, Chemistry, Computer Science, Earth Sciences, Economics, English, History, Math, Philosophy, Physics, Political Science, Psychology, Sociology.  Universities were scored as follows:  5 points for #1 programs, 4 points for programs ranked between second and fifth, 3 points for programs ranked between sixth and tenth, 2 points for programs ranked between eleventh and fifteenth, and 1 point for any additional program in the top twenty.  The results are not that different than in previous iterations, though I've not gone much beyond the top twenty since the metric, being weighted towards top programs, does a poor job distinguishing between research universities with considerable breadth, but few if any top ten programs. 

1.  Stanford University (69 total; ranked in the top ten in all 16 areas; six #1 programs)

2.  Harvard University (64 total; ranked in the top twenty in all 16 areas; 15 top ten programs; six #1 programs)

3.  University of California, Berkeley (61 total; ranked in the top ten in 15 areas [no medical school at Berkeley]; six #1 programs)

4.  Yale University (49 total; ranked in the top twenty in 15 of 16 areas; 11 top ten programs; three #1 programs)

5.  Princeton university (48 total; ranked in the top fifteen in 13 of 16 areas [no medical, law, or business at Princeton]; 11 top ten programs; four #1 programs)

6.  Massachussetts Institute of Technology (46 total; ranked in 11 of 16 areas [no medicine, law]; 10 top ten programs; six #1 programs)

6.  University of Michigan, Ann Arbor (46 total; ranked in the top twenty in all 16 areas; 10 top ten programs; one #1 program)

8.  Columbia University (45 total; ranked in the top twenty in all 16 areas; 11 top ten programs; zero #1 programs)

9.  University of Chicago (40 total; ranked in the top twenty in all 16 areas; 8 top ten programs; one #1 program)

10. University of California, Los Angeles (37 total; ranked in the top twenty in all 16 areas; 6 top ten programs; zero #1 programs)

11. University of Pennsylvania (31 total; ranked in the top twenty in 14 of 16 areas; 6 top ten programs; one #1 program)

12. Cornell University (25 total; ranked in the top twenty in 14 of 16 areas; 4 top ten programs; zero #1 programs)

13. University of Texas, Austin (24 total; ranked in the top twenty in 13 of 16 areas; 3 top ten programs; zero #1 programs)

13. University of Wisconsin, Madison (24 total; ranked in the top twenty in 12 of 16 areas; 3 top ten programs; zero #1 programs)

15. California Institute of Technology (23 total; ranked in the top twenty in 6 of 16 areas; 5 top ten programs; two #1 programs)

16. New York University (22 total; ranked in the top twenty in 10 of 16 areas; 3 top ten programs; one #1 program)

16. Northwestern University (22 total; ranked in the top twenty in 10 of 16 areas; 5 top ten programs; zero #1 programs)

18. Duke University (21 total; ranked in the top twenty in 11 of 16 areas; 3 top ten programs; zero #1 programs)

19. University of California, San Diego (15 total; ranked in the top twenty in 9 of 16 areas; 1 top ten program; zero #1 programs) 

19. University of North Carolina, Chapel Hill (15 total; ranked in the top twenty in 8 of 16 areas; 1 top ten program; zero #1 programs)

Runners-up for the top twenty:

University of Illinois, Urbana-Champaign (14 total; ranked in the top twenty in 5 of 16 areas; 4 top ten programs; zero #1 programs)

Johns Hopkins University (13 total; ranked in the top twenty in 5 of 16 areas; 2 top ten programs (both top five); zero #1 programs)