The UCSF-UCB program is a joint program where, after five year, you graduate with a M.S from UC Berkeley and an M.D. from UCSF. The first three years (the preclinical years) are spent across the bay in Berkeley where 12 students learn the material required for clerkships (and step 1 of the boards) pretty much exclusively with PBL. They have clinical coursework as well that grants them early exposure to interviewing patients, physical examinations, etc. A large part of the third year is about getting your Master's Thesis in order and preparing for Step 1 of the boards. After completing the three years at Berkeley, most move over here for clerkships and fourth year. It seems like an interesting program and I contemplated applying to it, but decided that I wasn't really into that philosophy so much.
I guess the major differences between the UCSF and the UCSF-UCB programs are class size and proximity to the hospitals. I don't think I'd be as happy as I am with my class of 140 if I were to have to be in a class of 12. Yes, you'd become incredibly close with those people, but I really appreciate having a fairly large class of people. We have small group sessions with around 12 people and if my whole preclinical education was like my small group, I don't think I'd get as much out of my education. Secondly, I think there is something to be said about attending a school that is attached to a large teaching hospital. Not only are there more opportunities to shadow as first years, but I think that spending time around a campus that is in a large health care center was something that I was looking for. Many of our clinical lectures are given by the heads of their respective departments. It is pretty cool to have the head of the cardiac catheterization lab give you a lecture on care of the acutely ill cardiac patients, etc. The pathology department here is amazing, and I have been really impressed with the faculty who have lectured us. Faculty from the VA and SFGH also lecture quite a bit. I don't know, I just think being closer to all of the UCSF-based hospitals has many advantages.
I have a very good friend who is in her third year of the UCB progam and she liked it, but I think that I wouldn't enjoy it as much.
If you want a M.S., enjoy the idea of spending three years with 11 other people, and really really like PBL without many lectures - then go for it.