I'm kind of wondering about this too. THis is currently part of my dilemma in figuring out how to rank programs. I currently have 3 that I really liked and was really impressed with, and am considering ranking #1 (although there are others that also impressed me a lot).
My thoughts: Big programs are somewhat more important if you are seriously contemplating an academic career, as you will make connections with people that are more well known nationally, and there will be more opportunities for research and further study. You also will see more difficult cases and consults, and be towards the forefront of trends in diagnostics, etc.
Smaller programs may generally have more of a collegial atmosphere, and more one-on-one attention. In fact, sometimes I think it might be easier to get involved in research projects at smaller places because there won't be as much competing for your attention (or the staff's attention). Small programs also tend to have to reputation of training generalists, (i.e. private practice) while larger programs can steer you more towards academics and specialty careers.
That being said, many people will end up doing a fellowship (or more) after residency, and even if you decide to go to a smaller program, if you are a smart and talented resident you can probably just go do a fellowship at Johns Hopkins, for example, and have many of the same opportunities, if not more, as someone who did their general residency there. Of course, many large prestigious programs do tend to favor people from their own training program for fellowships.
For someone like me who is interested in academics but has no specific career path beyond that in mind yet, a larger program may provide advantages, according to some pathologists I have talked to. But others have said that smaller programs may provide more of an opportunity to shine, and then be positioned for a top-notch fellowship. I have heard criticisms of some of the bigger programs in that the residents somewhat get "lost" in the shuffle and have to take more initiative on their own, and the volume is quite high so most of their day is spent doing work. Number of calls doesn't concern me that much so I haven't focused on it. As long as it isn't too malignant I will deal with it.
So, I don't know. I am still debating this with myself. I would say, however, that be careful what you mean by a "small" program. There is such a thing as too small. Pathology training does depend a lot on specimen and lab volume. A large referral-type hospital is more important.