I'm not entirely sure, to be honest; I guess it depends on the concentration. I'm in a pretty non-traditional one as far as YDS goes (Asian Religions). 2 of us applied to PhD programs this year and we both got in to our top choices, so I guess that bodes well. If you're interested in doing a concentrated MAR, it's important to remember that you have the resources of the larger university at your disposal. I take half of my classes at the Divinity School and half "downtown" (in other words, not at the Div school - for me, it was mostly at the Dept. of Religious Studies, but people do other things as well). You have much more flexibility in terms of how you design your course of study in the concentrations, since it's mostly up to you and your advisor (I think everyone has to take two bible study classes and 4 semesters of language, but the rest is open). This helps when it comes time to apply to PhD programs, since you'll have completed coursework and written papers that are more in line with your interests. Of course, it's also helpful that you'll be able to get good letters of recommendation from well-known faculty. This is not to say that the Divinity School alone doesn't provide enough opportunities to do this, but it's something to keep in mind.
So, I guess, to sum it up - I'm not sure how it compares to places like Harvard or Chicago, but you wouldn't be closing doors that would otherwise be open by going to YDS.