1: UPENN: Top 5, great fellowship placement, great training, great research, it's just great...but philly kinda sucks (IMHO)
2. UW: 3 hospital system, great academic rep, great clinical training. Only problem is you get lost because the program is so big. Fellowship placement is really really good too.
3. UChicago vs UCLA vs. Mayo vs WashU vs Michigan vs Cornell
These are all relative equals in academic rep and fellowship placement. (Wash U has better rep for med school than IM, it's relatively an easy match for IM for many reasons described in other posts). I think this will come to personal preference based on your interview experiences and location preferences. You can't really rank these programs reliably.
As far as my personal prefernces: 1) UCLA 2) Cornell 3) UChicago 4) Mayo 5) Washu 6) Michigan
As far as UCSD, BIDMC, UAB, Northwestern, Emory: I believe this are small notch below the ones listed above in IM, but still overall outstanding programs, top 20ish. BIDMC wouldn't be so great if it weren't affiliated w/ Harvard. UCSD has fellowship placement that is relatively weak in Cards but it offers great IM clinical training. UAB's name isn't as good as the program actually is, though it is top 10 in Cards. Northwestern has a rep for being Cush, which can haunt you in academics. Emory has Grady (County) so great autonomy. They also have a great Cards program.