As long as the residency is accredited, the "prestige" associated with it doesn't really matter in hiring - at lease not in my experience.
What matters is what you've done in the residency - the projects you've taken on and how well you've done with them, as well as what your supervisors and mentors have to say about you.
All candidates will require some training to get up to speed in the clinic, but when I'm on a hiring committee I need to know how quickly the candidate will become independent. Can she be trusted to sign off on a treatment plan? Can he clear a dosimetry interlock (and know the difference between entering the password and assessing the problem)? Can she take the lead on the purchase and commissioning of a new unit? All accredited residencies will provide training in this kind of stuff, but what we try to assess in the interview process goes beyond simply having been trained in the field and more towards each candidates performance level, independence, and ability to confront new problems - if that makes sense.
Each residency will have it's strengths. University-based ones are more likely to have opportunities for involvement with research projects. Even if you lean more towards the clinical side of the academic-clinical spectrum, these can be the kind of thing that can land you that first job because they can give you direct experience with the new technologies that many smaller clinics will be interested in adopting in the "near future." From a networking point of view they are likely to have had more graduates and the professors are likely to have more contacts, which may help in finding that first position.
Physics group residencies may be more likely to involve more commissioning work, which can be a huge bonus in my opinion. You learn a lot more commissioning a new unit than you do performing routine QA on it month after month. Also, depending on the group, they may offer exposure to multiple sites, which means you'll see more than one way of doing things and can help from a networking perspective as well.