Are you asking about Integrated or Independent residency training programs? Some of the "biggies" are in Texas - UT Southwestern, Baylor and UTMB. Also Emory, UCLA, Duke and Pittsburgh would be considered "biggies" as well.
As you know, reputations vary temporally and any chairman will have different opinions about which programs are among the best. That being said, the programs most frequently mentioned by reputation are:
nyu (largely because of mccarthy)
harvard combined program
As previously pointed out however, reputations don't always translate into training. There are certain programs such as loma linda and siu, that don't carry the same reputations as those above yet provide phenomenal training according to residents I talked to on the trail.
Does anyone know if there's a general trend towards cutting integrated programs out? I know that I've heard lots of rumors that our (Duke's) integrated program is going to be scraped (which means that our SEVEN year Gen Surg Program becomes the pre-req for Plastics), but I don't know if they're getting rid of similar programs across the country.
I don't know that its necessarily a trend per se, but several high profile programs have dropped their integrated programs in recent years (NYU,Emory, & most recently Duke Univ.) Most of the complaints I understand had to do with 1) instability of the program due to a high dropout rate & 2) the lack of preparedness of the residents after their preliminary years. Seeing as how the driving force for integrated programs is financial & that the economics haven't changed, it's unlikely that a large # of programs would drop their integrated program b/c they can't afford to.