Whew... that might take me a very long time. When I started the process, I was not very confident about the strength of my application at all. And as a California resident, I didn't have any "safety" state schools to apply to. So I ended up applying to far too many schools--I applied to 25 MD/PhD programs (including programs from the top-20, most of which are MSTP), and 2 additional MD-only programs.
It would take far too much time to describe which programs I applied to. It is true that the whole process is a crapshoot--you never really know what programs will accept you, so I still contend that it's nice to have safety margin of applying to additional programs. I do want to mention, though, that applying to 25 programs was FAR excessive for me. Not only did I rush through all these applications (all 25 were completed in 2 weeks), what ended up happening was that once I got into my first medical school in mid-October, I withdrew from all but 12 of the programs.
So basically, I ended up going to 13 interviews. I suppose I can comment on the strengths/weaknesses of these programs, but I think that it is best for you to find out yourself. That is because each program is unique in many ways, and what appeals to one person may not appeal to the other. There are many factors to consider. If you like smaller programs with more individualized attention, for example, or if you would prefer a larger program with more representation in the medical school. If you like the medical school to be associated with the undergrad community. If your field of research is particularly strong at one school. If you prefer one location in the country over the other. If you prefer urban settings or more rural, small-town atmosphere. If you a greater emphasis on learning clinical medicine or research... all these are factors that you yourself must take into account when you are applying to the programs.
You will notice that there is no official "ranking" of the MD/PhD programs, and that is precisely because each program has a different set of attributes, be it strength of research in one field or the other, or just location and general atmosphere. You have to pick the program that is the best for you. Of course, I mean to apply to a lot of programs that appear like they might suit you. An MD/PhD from any of the top programs or any MSTP/combined degree program will lead you to the same place professionally. So all you need to to do is to wait until the interview and/or revisit to see if the program is good for you personally. You will learn a lot more about the faculty and students during the interview, and hopefully during the interview you can learn for yourself the strengths and weaknesses of the program and whether the program suits you.