I think that everyone has been in your position at one point or another, so don't panic! You still have plenty of time to figure all of this stuff out.
If you're not really sure what to look for in a program, then I would recommend taking a few days or so and reading up on past posts in this forum. If you don't even know where to start, then I would recommend the legendary
MSTP Boulevard thread; this is what I did when I was in your very same position. Although the thread is almost four years old now, it's great since it is essentially a complete walkthrough of the application process for one year's group of applicants (and a decent number of these people are still regulars on this forum). A lot of really important issues are discussed and reading that thread is a great way to begin thinking about the MSTP application process (just keep in mind that some of the specific details of the programs, such as number of spots, may have changed since then).
I'd also recommend checking out some of the School A vs. School B threads to see what others place emphasis on when making their decisions. By doing that you should be able to start forming more opinions on what factors are important to you and what you really don't care about (at least for now). For example, some MSTP applicants don't weight the med school that much in making their decision since they think in the long run the calibre or philosophy of the medical school doesn't matter as much as the grad school and that most medical schools give an equal education. You should also think about how much emphasis you want to put on the med school sides of things versus grad school.
This is how I went about deciding on schools:
I asked several of my mentors about what schools were particularly strong in my certain areas of research interest. I then cross-checked these schools against the list of MSTP and non-MSTP MD/PhD schools. I added to this list of schools the programs that were highly talked about (and that I seemed interested in) on the forums and the intransit.us site. I also added a couple of other schools that seemed like they might make for decent 'safety' schools.
For each of those schools, I spent some time reading through the research descriptions of the neuroscience faculty to get a feel for what areas of research were popular at each school and for how many profs were doing research in my areas of interest. Since I wasn't absolutely sure what area of neuroscience I wanted to go in to, I decided that to primarily look for schools that had at least a few faculty members doing research that interested me in my current areas of interested but that also had a fairly diverse and strong neuro program overall.
I then started to look in to the other factors: strength of the med school, strength/size/age of the MD/PhD program, location, etc., etc. to continue eliminating schools until I had a reasonaly-sized list.
Everyone has their own method, but maybe that will give you some ideas. My main piece of advice, though, is to read up on past posts and start deciding on what you ideally would like in a (a) grad school, (b) med school, and (c) MST Program. Which of these three areas are most important is a personal decision, and it's probably a good idea to have that figured out before spending too much time looking into individual programs.
Anyway, best of luck! I hope that this helps somewhat.
