I think that many of the traditional differences between community-hospital and university residencies are rapidly disappearing or becoming irrelevant. In the past, there was a big distinction between the university hospital, with a high volume of complex referral cases, salaried professors, big-time research, etc. and the small, low-volume community program with volunteer private faculty, no research, and bread-and-butter cases. But with the way hospitals are run these days, virtually all programs will be a hybrid of university and private.
A lot of University hospitals have seen their patient bases shrink as managed-care affects referral patterns, and "university" residents may get a large percentage of their cases at rotations on private services at outlying hospitals. And in fact, many university hospitals have been bought out by private hospital systems (i.e. Georgetown by Medstar), so a hospital with University in the name may not function like a traditional university hospital at all. Conversely, in some areas large private hospitals dominate the market, and actually do a higher volume of complex tertiary referral cases than the local university (Inova Fairfax in northern Virginia comes to mind). They may be involved in clinical trials, take level I trauma, and do tons of Whipple procedures just like the university.
I trained in general surgery at a program with university in the name, but which was really based at three large community hospitals. There was a mix of salaried and private-practice attendings, some of whom were great teachers and some of whom were terrible. But frankly, the ability to teach well wasnt always directly related to where the money came from. For fellowship, I trained at Baylor College of Medicine, which has the reputation of being a very traditional university program. But here, the residents spent much of their time at Methodist Hospital, which was very much a private institution, with an attending-does-case-while-resident-holds-retractor culture.
As far as I can tell, the traditional academic practice is a thing of the past. The academic surgeons are under just as much pressure to increase billing as everyone else. Everyone is hustling for referrals, worried about managed care, and competing with the hospital down the street. The last bastion of the traditional hierarchy may be a county hospital or VA environment where all you have is indigent patients.
Sorry for the long post, but 'University program vs. community program' just seems to me like a false dichotomy in most cases.