All EM programs have a different flavor.
Some programs are stronger in others in certain regards. Some programs have more trauma, some have more peds. In some places, attendings control the ED, others are more resident-run. In order to find out more info, you can go to SAEM website and talk to residents from that program.
There are a few programs that are listed as 'Top' programs, but everyone's list differs. In general, there are a few programs that consistantly make the top of the list, usually based on the research reputation of the faculty: Denver, Hennepin, USC, Highland, Jacobi, Bellevue, Pitt to name a few. These programs definately have their strengths and weaknesses as well.
Like many have said, your best bet to become the best doctor you can be is choose a program where you'll be happy.