i have the impression that a number of people chose to go to BID (bias: rising CA-1) partially because it is a harvard hospital and in years past they have had better board scores than brigham and MGH...but I would bet "MGH" carries more punch on shear name recognition.
yale seems to not get much love on the 'net...i can't say i could tell you why. maybe b/c new haven is not too happening for most people, but cheaper than boston on nyc.
also, where do you want to practice? name recognition is much more important within a given region (ie, emory in GA)
listen to those on this forum wiser than you. privelege location and program fit much more than name recognition