it depends on what you want, Johnisit1234. Both schools are very good, with Emory having the edge on reputation. What you need to decide for yourself is what place would you be happier at? If you want to go into something like derm or ortho, maybe going to Emory would help in terms of name recognition.
Someone commented above that Emory's match list isn't all too great. Realize for this that close to half of Emory's students are Georgia residents and may want to remain in Georgia for their residencies. Close to 40% of last years class remained at Emory for residency and this could be because of recognition, because they liked Emory, because they wanted to stay in geogia, among other reasons.
MCG doesn't post their match list (if anyone has it online, please post!), but it's nothing to be ashamed at, at all. From what they told us at the interviews, the majority do remain in Georgia -- they have some sense of GA loyalty. I'm assuming many probably end up going to Emory or staying at MCG for their residencies.
Truthfully, I don't think you can go wrong with either choice. While Emory seems to be killing the poll above, meanderson's comment about it is true. If the pricetag isn't important to you and you're not interested in academic medicine, choose the school you'll be happier at, or that you got the 'best' feel for.