You think?
Emory was probably the most heavily research based of any of the programs I looked at. MUSC had that component for sure, but not to the point of Emory. They just seemed more clinical at MUSC, and the residents seemed to have more of that focus from my perspective. It seemed like almost no one at Emory was interested in anything but a fellowship after residency.
MUSC uses a night float system in place of call, so you essentially know when you're going to be on. Emory has a more traditional call system going into your third year.
The benefits seem to be better at MUSC than at any other program I visited. They take care of your parking, give you a stipdend for academic uses, as I recall, pay for your healthcare. You also earn extra days off if you round past 1 on the weekends.
There's the fact that all of MUSC's hospitals are all there right together. At Emory, they're spread all over eternity.
At MUSC, you have a metro area of about 450,000 people. At Emory, you're looking at 5-million. You have historical ambience in Charleston combined with the beaches and cuisine of the Low Country. You have a major metropolitan area in Atlanta with all the benefits that come along with that.
There's also the general impressions of the place. I got the impression that MUSC tended to have a more layed back and conservative political bent. Emory seemed far more snooty/liberal in my eyes.
If you're looking at having a family, realize the schools in both areas are sketch. There are places you can find that have good public schools in the areas, but they're pricey. Almost prohibitively pricey around Charleston.
Hope that helps a bit.
Others may have a opinions that vary, but I thought I'd get the ball rolling.
I never visited Duke, so I couldn't help you ther.