This depends on your specialty and your career goals. In some specialties some of the most prestigious residencies are indeed community based. (I'm told OB/GYN is like this, although not being one, I can't confirm) Likewise the more competitive the specialty, the more likely having an academic affiliation will help you, with a few exceptions, some sub-specialties seem to have a community based program tilt (for example Colon and Rectal Surgery).
That being said...my advice is going to sound incredibly unhelpful but I'm going to say it anyway, Go with your heart. Being miserable at the #1 program (if there ever was such a thing) in your field will almost certainly mean that you will not thrive as a person and thus not excel as a resident, which will ruin your chances far quicker than going to any community program (almost). Imagine having the most respected guy in the subspecialty you want to enter think you are a dolt! That can't be good. On the other hand, if you go to a quality community based program that is smart enough to get you the exposure that you need to the people you need to meet (I can think of many community based programs that have allowed their residents to either rotate away, or go away for research to gain exposure) and you are "the best resident they ever had" because you _love_ it there, you will have a fighting chance. Will you be fighting an uphill battle by not going to a Big-Name program? Yes. The way I see it though, if you love what you do and the people you do it with, then you can't go wrong.
As far as job after residency: I would say that if you want an university based academic job, then it is hands down much easier to score one from a University based program. Assuming that you (like the majority of people) want to enter private practice, I would say that the job market is more limited geographically in community programs (their alumni based isn't usually nationwide) but otherwise they generally find excellent practice opportunities.
Hope this helps you.
