First of all, let me start by saying that I am a nontraditional applicant with high stats and I am interested in both MD and DO schools. I honestly don't care what letters are behind my name, because I believe that letters don't make someone a good doctor. I think both degrees have their strengths, and my goal is to get into a school where my family and myself will be the most happy. I also applied to A BUNCH of schools because flexibility was very important. Before the process started I decided that I would apply to 10 DO schools and 30 MD schools.
I used a process of elimination to select my school list. I did this by buying both sets of books and flagging each school with a post-it. When I eliminated a school I took the flag off. Note that in the list below, the number of schools left 'in the running' will be presented by (x), these are estimates because I chucked the notes I was using. They will be MD and DO respectively.
1. Bought MD and DO books from AAMC and AACOM. Flagged them. (126) (26)
2. Eliminated 'high stat schools' where I don't have a chance. (118) (26)
3. Eliminated schools in states where I/wife have no desire to live. (90) (19)
4. Eliminated schools in cities where I/wife have no desire to live. (75) (12)
-At this point I took a few minutes reading about all of the schools. I evaluated my desire to go there and ranked it low, mid, high. I also mentally ranked my chances of getting in because of IS preference, stat requirements, prerequisite requirements, and so on. These were also ranked low, mid, high. I created a basic rating rubric for this part and I think it worked pretty well.
5. Eliminated all schools with both LOW CHANCE and LOW/MID DESIRE. (50) (10)
6. Eliminated schools with ludicrously high tuition. (40) (8)
7. Selected 30 MD - 25% safety, 50% good chance, and 25% reach schools.
This ultimately brought me to right at my goals of 30 and 10. My strategy was to apply early to all potential schools and then prune them as things progressed. In other words, I set myself up for success and THEN started to look at the strengths/attributes of the schools listed above - apply early!!! I sent in my secondaries as I received them with some bias to schools that I prefered. I read up on all the schools more thoroughly at this point, and after I started receiving interviews at schools that I liked both academically and 'lifewise', I started ignoring secondaries from schools that didn't interest me. Ultimately I ended up being complete at 20 MD schools and only 3 DO schools. Mostly this is because the DO schools took too long to get back to me and I was running out of secondary money so I had to prioritize and go with the ones that I really liked.
I hope this helps!
Edit: In my opinion, geographic preference is probably the most important part of selecting a school. It is impossible to learn and live a happy life in a place where you are miserable.
Edit2: Also - the DO schools I ended up applying to were my favorite ones - PCOM, LECOM and UMDNJ.