I find myself in this boat. As a competive applicant, there is pressure to choose a top/research program. For me however, research is less important and I desire more time with my soon to grow family. Since I wish to go into private practice, I feel I can be very well trained at a smaller university hospital with less stress. Can anybody relate?
Go where you're happy. I had the same situation, went to a tiny community program (in # of residents only.. the volume was enormous and we all learned how to be extremely efficient) had time to write papers, get on committees, network within and without my home area and got interviews and offers at two of the top programs in my field (only interviewed at two places b/c the jobs were basically mine for the asking before the interview. Another thread discusses why this has to happen). I'll also add that I loved my job, my attendings and most of my colleagues, and the life I had a chance to live outside the hospital walls.
Poeple that interact with you WILL notice if you're happy in your job. They WILL want to work with you. If you go to someplace small just make sure you attend meetings, be active in ASCP, USCAP and CAP in whatever way you can and get yourself in front of people in the field you want. If you can go where the attendings do things like this too. CAP/USCAP/ASCP is not exclusively run by academic people.. in fact because of the spare time that community practice DOES give people there are more private practice pathologists involved in these organizations than you might guess. Additionally, if you work well enough, YOU can help make the name for where you go. That is never mentioned on this forum. It's all about going where other names are, as if there is no chance at all for you to contribute to the excellence and reputation of your program. I would say don't sell yourself short by assuming (as most here do) that the only factors contributing to your success are going to be the names you're surrounded by and not your own skill. (in fact I'd be weary of people who say this - basically admitting they have nothing to offer pathology besides their associations)
You will also likely learn better when you're happy, do better work, not worry about the job you think you're entitled to because you have a name behind your training, and you'll likely get whatever fellowship you want, regardless of what people here say. The people that followed the model I just described at my program got fellowships or fellowship offers at Pitt, MD Anderson, Mayo, UCLA, John's Hopkins, etc.
EDIT: That last paragraph could be read to contradict my point that big names aren't as important as people make them. I was trying to say that you're not denying yourself good post residency training at "big names" if you don't go to one for residency. Also, I should add that some residents who got offers at big name fellowships continued to accept offers at "smaller" programs for fellowship, did well, and got the jobs they wanted.