Update (2016 Mar 9). The OP asks (emphasis added):
Is there a guide to selecting a math education graduate program, including a reasonably comprehensive list of programs?
Here is a List of Links to U.S. Doctoral Programs with a focus on Mathematics Education.
The linked google spreadsheet was generously compiled by Kenneth Bradfield with the assistance of a few others (click through for attribution) and contains the following headers:
At the time of this update, there are 110 different institutions listed.
The most recent approximation of rankings (of which I am aware) is available here.
Note that it only concerns the United States, and that the article is from 2007. Its citation is:
Reys, R., Glasgow, R., Teuscher, D., & Nevels, N. (2007). Doctoral programs in mathematics education in the United States: 2007 status report. Notices of the American.
The relevant chart:
Disclaimer: A fair amount has changed in the intervening years, and there are surely more changes in store for the future. Moreover, the value of a program will depend in some major way on the professors with whom you work, and the subject of your research. It may also be worth noting that the demand for those with doctorates in Mathematics Education is quite high (Inside Higher Education 2013 piece and related AMS notices 2013 pdf) and federal funding seems to be increasingly available for work in education (at the graduate level: an example is the extension of the NSFGRFP to STEM Education). Lastly, it seems clear that the Common Core State Standards (2010) and the retirement of older faculty members (who are prominent at some of these institutions) are both likely to have influenced these rankings.
FWIW: Since the National Science Foundation began granting fellowships for graduate research in Mathematics Education in 2011, students at the following institutions have received them:
2015: Morehouse College; University of California-Los Angeles; North Carolina Agricultural & Technical State University; University of Texas at Austin; University of California-Berkeley
2014: Michigan State University; University of Minnesota-Twin Cities
2012: University of California-Berkeley
2011: University of California-Irvine; University of Illinois at Chicago; Northwestern University; Teachers College, Columbia University
Listed above are award offers strictly in STEM Education and Learning Research - Mathematics Education. For more information, see NSF FastLane :: GRFP.