That's a tough call ...
I'm at Tulane, and I like it. The two schools are really similar: urban schools with public/county and private hospitals, both have great clinical years, and both are rather traditional in curriculum. Both are in neat cities, but I think I might like ATL better purely 'cause of the cultural diversity ... but N.O. is great, cause of the food and music.
I think the major difference is that Emory is, well, to put it simply "known". Everyone knows that it's a great school, and US News feels that way, and they have a ton of research money. I have no idea how the students feel there or if it's a good place to go to school, but I just know that when I hear Emory, I know it's a great place. Tulane, on the other hand, is 'known' perhaps best just regionally, in the South.
Go where you will feel the most comfortable ... both are great schools.
Simul