Dnt,
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)
emory
pittsburgh
michigan
southwestern
baylor
ucla
harvard combined program
yale
hopkins
wash u
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.