Yeah, I've thought a bit about the whole reputation thing, and I'm still not sure how Mayo is perceived by others. Opinions I've heard from patients and doctors alike range from "oh, that's the local hospital, I guess they're OK" to amazing. One cardiology fellow I met at a national meeting told me flat out that I'd get ranked to match at a number of the lesser cardiology fellowships simply because of the Mayo name. Clearly the cardiology fellowship program likes Mayo-trained residents. One of the residents heading elsewhere is going for family reasons, not sure about the rest. Mayo certainly has name recognition, but I get the impression that some of the less informed people outside of academic subspecialty areas don't realize just how much of a major academic medical center it is. We're technically not a university program, but there certainly are very active basic and clinical research labs, a variety of health science students around, and a healthy academic environment. Of the faculty I talked with at my med school, nobody thought I'd be harming my academic future by going to Mayo, some thought that Mayo was amazing and I'd be foolish to not rank it highly, and some of them preferred other well-known programs over Mayo. There are some myths about Mayo out there (probably the biggest myth is the "fellow run" thing, which as I've attempted to point out before, couldn't be farther from the truth if for no other reason is you simply don't work with fellows that often; some people think Mayo is a "community program" which is just silly).
So, in the end, I'm still not sure if Mayo gets due credit. When I was interviewing I certainly felt that it was one of the top residencies in the country, and while I would say the reputation is generally very good, I sense a bit of anti-Midwest and anti-non-University sentiment at times.