After agonizing over this question myself last year, I came to a few realizations (with the help of ideas from various others).
The biggest difference med schools will try and push on you is PBL vs. Lecture based. Nowadays, every school is advertising some type of PBL. Its up to you to figure out EXACTLY what they mean. I would say a few of the only schools that are truly PBL schools are Cornell, Northwestern, Cleveland Clinic, and SIU. Everyone else will have PBL style small group discussions, or seminars, but its not as big a part of the curriculum (ie not everyday for 3 hours) as at the aformentioned places.
My take on PBL vs. Lecture is that ultimately it doesn't matter one way or another. Each has its advantages and disadvantages. If you don't like group work, stay away from PBL. If you do better by skipping class and studying by yourself, go to lecture based. People will say PBL is so great because you have only x hours of class, then the rest of the day. Well guess what, you have the rest of the day, but a decent amount of that time needs to be spent studying independently on stuff you didn't talk about in PBL group. You can effectively do something similar at lecture schools by not going to the boring/uninteresting classes and covering the material yourself, especially if they have transcription services, recorded lectures, slides, outlines, etc available.
Yes, PBL will probably train your critical thinking/problem solving skills. Not to say you can't have the same thing in lecture based schools. People will say PBL schools require more time studying for boards because they may have missed something because of the fact that their PBL group went a certain direction with a case. This is probably true, but everyone needs to study a lot for boards, regardless of curriculum style.
I guess what I am trying to say here, is that ultimately PBL vs lecture really doesn't matter (Unless you have some huge aversion to group work). There are many other factors in choosing a med school that are more important, and will have a bigger impact on you experience.
One of these is P/F vs. graded. I think this is a much more important element of curriculum. And don't schools fool you, there is no difference between F/LP/P/HP/H and F/D/C/B/A. Even F/P/H isn't as desireable. I think that anything beyond straight P/F is asking for competitive behavior. Yes, people are competitive everywhere, even in schools with P/F. But why give people who are by nature competitive to be even more competitive and cut throat? For me, having a P/F system was definitely something I was looking for in a school, and it did factor into my decision of where to go. I just think that its easier to learn when you can focus on getting through the material to understand and learning, rather than panicing over whether I need to do better than some other people so I can get honors.
True, some places may keep records of actual scores for AOA and class rankings for dean's letters, but at least its not thrown in your face every week. Now if you are not the self motivating type, and think you will just do enough to pass in a P/F, then it might not work out very well. But generally, I think P/F is a great thing, and something that will definitely affect your med school experience.
Ok, sorry for that diatribe. I am bored at work and needed something to do.