Here are few thoughts I had regarding some of the places I interviewed which have not been mentioned in this thread. I won't really comment on global health as this was not a major factor for me.
Mount Sinai: I really liked this program. It is 2 years but most fellows stay for 3 years or more. The program director, Dr. Shirish S. Huprikar, is very involved and dedicated. The clinical year is one of the most diverse in the country thanks to the inclusion of Elmhurst. There is also a very large transplant service at Mount Sinai. There are many research opportunities and the medical school is in the process of building a brand new research building at the main campus. Thus far fellows have had no difficulty staying for a third year of fellowship. I think that this is currently the best program in New York.
NYPH Columbia: This program is clearly strong and produced excellent ID fellows. The patient population is quite diverse and located in a predominantly hispanic (Dominican) part of NYC. Clinically they are presently lacking a bone marrow transplant population but it sounds like that may change soon. Many transplant patients are seen by private attendings without incorporating the fellows. There is only one teaching ID consult service which is run by one attending and two fellows. The program can be flexible and provide those clinical experiences by allowing fellows to rotate outside Presbyterian. The fellowship program appears to be primarily run by recent graduates. Because they are a smaller program there is some limitation in research, however, the research that is being performed at Columbia is quite impressive. Fellows may either audit or formally attend the school of public health.
UCLA: This is probably the best location if you're primarily interested in Transplant ID. Fellows spend the vast majority at Reagan which is described as a "quaternary" medical center. The program invests a significant amount of funding in their fellows supporting a PhD or masters degree depending on your interests. Fellows have no difficulty staying for four or five years. On the other hand, they've also been able to easily adapt their schedule to those fellows who decide not to perform research and it is possible to finish in two years. ID fellows do spend a month or so at Santa Monica Medical Center for some bread and butter ID. The program director admitted that the program had been in decline before he took it over and he is now trying to rebuild it. He is planning to hire a third ID fellow. I think that they could easily support five fellows and create a broader clinical experience by spreading the fellows out across more hospitals during the first year.
Emory: The clinical experience is very diverse thanks to Grady Hospital and the opportunity to see patients in a more community style at Midtown which also offers obstetrics services. Grady Memorial provides an amazing clinical experience for fellows and now has an electronic medical record. Dr. Armstrong is extremely dedicated to the fellowship program and keeps close tabs on her fellows. In general fellows stay for a third year. Emory keeps many of their own fellows as junior faculty for additional nurturing after completion of their fellowship. The program is very large and there are a ton of opportunities for research, almost too many. In addition to 50+ faculty at Emory, Fellows have the opportunity to work with mentors at the CDC as well. The option is available to earn an MPH or MSCR during the 2nd or 3rd year.