Here are some factors other than Location, Reputation, and Cost, which as others said are the top factors for many applicants (including myself when I applied).
-curriculum format: there are several types of curricula as follows:
1)subject blocks: take one class at a time (e.g UMAB, UTMB)
2)integrated blocks: take several courses relevant to the same subject. For example, in Tufts' Infectious Diseases block during second year, we take Microbiology, Pharmacology of ID (antibiotics, anti-virals, etc.), and Pathophysiology of ID for 3 weeks then have 3 exams at the end of the block
3) organ-system blocks: students learn the anatomy, physiology, pathology, and pharmacology of each organ system all at once. I believe UCSF uses this system and second-year students at TUSM will be getting a taste of it next semester
4) PBL-students learn via cases in small groups rather than in lectures. Pitt, Harvard, and Rochester use this system, as does Drexel for students on a certain learning track.
5) traditional curriculum: students may take many non-integrated classes all at once, with lectures often running into the late afternoon. May be integrated with weekly PBL groups and small groups. This was Tufts' curriculum last year and I hated the long hours of lecture and lab during second semester, but for some people this type of curriculum works well.
-grading system: options are:
A/B/C/D/F- used by U Maryland, UF, and others I don't know
H/HP/P/F-a modified letter grade system (in disguise) used by NYMC, PSU, MCV/VCU
H/P/F-e.g Tufts, SLU, however, many schools change to H/HP/P/F during 3rd and 4th years
P/F-most of UC schools, USC, U Conn, Yale, Columbia, Harvard. oft. changes for 3rd/4th year.
grading systems have also been discussed ad nauseum on SDN, and each type of system has advantages and disadvantages. If you agree with the philosophy "P=M.D." for the first 2 years, then grades used by a school may be of particular interest to you.
-amount of clinical exposure during first 2 years:
I personally love being at a school that makes a huge effort to get students working with real patients during the pre-clinical period. There are a number of schools where students see only standardized patients (actors) like USUHS before going out on the wards in 3rd year (I have a friend there who can verify this). try to find out as much as you can from sources other than SDN if you are seriously considering attending a given school.
-general environment at the school:
are a number of social events scheduled throughout the year? do students seem to get along with each other and cooperate in the sharing of information via e-mail, handouts, etc.? does the administration show an interest in the school and the students and open its doors? just a few things to think about.. also, you may want to find out if people of your gender, marital status, race, sexual orientation, etc. are generally treated respectfully or if serious problems have arisen in the past.
-facilities:
does the school have the computer and library facilities necessary to accomodate med student needs? are the lecture halls reasonably clean, pleasant, and new? is the anatomy lab well-ventilated? how many people to a cadaver (some schools are outrageous with >10 ppl/cadaver)? is the school affiliated with reputable, clean hospitals with high standards for patient care? are the majority of affiliated hospitals reasonably accessible by public transportation or car?
hope this is of some help, I have talked for too long. good luck!