Here are my rankings of IM programs. These are just my rankings. However, I just finished the interview process and I tried my best to do as much research as I could into the "best" programs. This is my list but it is based upon a lot of resources (the advice of my advisors, the advice of my interviewers, the program directors at hopkins, mgh, and michigan among others, and finally the advice and experience of my fellow medical students and the interns I know).
Keep in mind though that the "best" program is the one that will allow you to maximize your learning to your potential. So, take the advice of people on this board and those around you, but make your own list. Your opinion is the one that counts in the end.
I have ranked the programs by tier. The programs within a tier are too close to rank.
First Tier: Hopkins, Brigham, MGH. The best of the best. If you can go to one of these programs, leap at it.
Second Tier: UCSF, Duke, University of Pennsylvania, Columbia. All 4 of these programs are great but a very slight notch below the top 3. Just as an example: UCSF takes 7 people for cardiology fellowship each year. Last year 3 came from Brigham, 3 from MGH, and 1 from Hopkins. It was an aberation but I do think that the top 3 programs have a slight "name" advantage.
Third Tier: University of Washington, Washington University, Stanford, Michigan. These program are good porgrams. If you want a great learning environment, you can't go wrong with Stanford -- Great PD. If you want to do primary care or are interested in ID or Pulmonary, University of Washington (seattle) is great. All of these programs have fellowship placement as good as the schools in the second tier.
Fourth Tier: UAB, UTSW, Vanderbilt, Mayo (Rochester), University of Chicago, UCLA. All very solid programs. And if some cases (depending on what you want to do after residency) these programs might be better than those in the higher tiers. I really liked Mayo (Rochester). UAB and Duke are probably my top two schools in the south. Make sure to enquire into UCLA's fellowship programs. They require a lot of research if you stay at UCLA for fellowship.
Fifth Tier: Cornell, Emory, Northwestern. If you want to do Heme-Onc, you can't go wrong with Cornell. Same for Emory and Cardiology. Northwestern has a sweet call schedule and a great work environment. I ended up ranking Northwestern pretty highly on my rank order list.
Sixth Tier: Too many to list ... but places like UCSD, BID, Colorado, Mt. Sinai (New York), OHSU, University of Maryland, NYU. Some of these programs (UCSD) have a huge location advantage. You can see the beach from the hospital!