OP,
Disclaimer: I am a resident in one of the older programs.
I do not believe the old school programs are on a "downswing" based on the quality of the faculty, graduates, residents, or applicants, variables that predict reputation. The newer programs are definitely on a steep upward trajectory owing, in part, to their newness (i.e. if a program is new, it doesn't have any reputation so it must grow.). However, with the growing number of overall applicants, and therefore, the greater number of quality applicants one programs growth doesn't hurt other programs. It is very good for EM to have such high quality programs throughout the country.
The term "prestige" in the initial post threw me aback on my first reading. After some thought, I took it to mean a positive reputation. Reputation should be based on the product: what do the graduates do in their careers, what jobs do they get etc; in addition, consider the current residents when you interview. This can be hard to get a handle on as it is obviously nebulous and full of subjectivity. Program reputation should not be a primary concern as this will only get a graduate so far, then they must rely on their own reputation. As with anything in life, one will get out of residency what they put into it. I believe that clinical excellence can occur at every program in the country; it is up to the resident.
I do find the contrast between "academic" and "county" to be odd, however. In terms of research dollars from the NIH, one Ivy is in the top 25 (UPenn at #4). The second most flush program overall with NIH dollars is Emory which is obviously a heavily county program (NIH funding for 2009, see EM programs:
http://www.brimr.org/NIH_Awards/2009/NIH_Awards_2009.htm). The point is that every program is academic; they are all teaching and doing research. So, I am not sure what the above posters mean by this comparison. In terms of pt populations, "county" often translates to poor and under-served. Academic translates to lots of consultants to call. You will see plenty of complicated pts regardless of where you go: some will be transplants, some will be undifferentiated hypotension, some (gasp) will be trauma.
EMRocks, in terms of choosing the place you want to train, consider how you learn (this is important as programs have very different teaching styles), where you want to live (short-term and long-term-these may be different) and what your goals are then find the place that provides what you are looking for. I know it is easier said than done. You'll figure it out. I promise.
Good luck,
iride