From someone who is at a southern school, and have personal experience/friends at the country's top institutions. Note, I only applied to institutions in the first 2 groups, so my rankings on the bottom group is probably personally biased.
In terms of just measuring pure academic strength of the institution and the program (ie. this is how my advisor would put it):
1. Duke - 'nuff said. I put this first for its academic merit, but not necessarily the place I would rank that high myself.
2-6. (in no particular order, one can easily justify one over the other depending on what you like, trying to peck an order out of this group is really personal preference):
-UAB (really an overlooked program, but is definitely a medicine powerhouse that is strong across the board and belies it's state affliated status, from personal interview experience. Some even put UAB up with Duke as the best in the south in terms of objective measures of the prowess as an academic program, ie. 5th in NIH funding across the nation, 11th best by US News, etc. Obviously dont have the prestige of Duke, that's the only reason I am putting it down a notch.)
-Vandy (my home institution, major academic/research slant put forward recently by administration, relatively good in almost everything, but considerably weaker in cards. Perhaps a weaker general internal medicine training because of the new academic/research focus, from my personal experience.)
-UNC (Didn't apply here, but according to my advisor it belongs to this group. From what I have heard, strong in pulm crit care medicine, not as strong as Duke in cards/GI)
-UVa (smaller program of the more " personal, gentler" sort, going to check it out in a couple weeks)
-Emory (From personal interview experience, it's an up-and-coming large program that is rapidly becoming more academic, and is expanding from its spectrum of expertise from a heavy cardiology slant that is its trademark.)
7-8. Tulane, Wake
9. MCG
10. MCV
11. UWV
If I have a choice MYSELF of all these programs, take into consideration of everything including reputation, training, maligancy and location, I would rank it in the following order:
UVa, Vandy/UAB (really a toss-up for me right now, if I am not affliated with Vandy, I'd do UAB first), UNC, Duke, Emory, Wake, Tulane, not sure will even rank the rest....