Hmmm.... I understand your dilemma.
Unfortunately, my advice is one I wouldn't usually like myself.
Generally speaking, I'm not a big believer in brand names. I chose a completely unknown undergrad institution because I thought it was a better fit for me, and I was not proven wrong.
The problem with us, however - and by us I mean MD/PhD applicants - is that we are different by the virtue of our career plans. For any regular medical student who simply wants to practice, there would be little reason to go for the brand name. Unfortunately, if I learned anything in the last several years, and this last year in particular, it is that academia, and especially academic medicine, is ridiculously political and hung up on reputation. I certainly don't like it or agree with it, but I would be silly not to acknowledge it.
I think we all would be.
Presumably we are all in this mess now to gain access to one of the most elite and competitive fields in the world - academic medicine. Please don't confuse this with the reason or the motivation - I know we all have deeper reasons for wanting to become physician scientists. But the fact remains that the only environment where we will be able to prosper in our pursuits is academic medicine (I choose to ignore industry for the sake of the argument).
So, my point is, that, everything else being equal (and I again assume it is: finances are not an issue, it's not MD vs. MD/PhD debate, etc.), we have much more to gain from the reputations of our institutions than our MD counterparts. Now clearly, if going to a better reputation school would be so detrimental (because of the geography, personal reasons, lack of research mentors in a particular area, etc.) that it would clearly significantly affect your preformance, than it's a different situation.
I think we would all be wise (in scenarios described) to make minor sacrifices and go to the school with a better reputation in our fields.
Having said this, I really don't want this to turn into another "it's-not-true-you-get-a-better-education-at-a-brand-name-school" thread. That is not what I'm saying at all. There is no doubt that getting a combined degree in itself gives you unparallel education. I am just pointing out that, given a choice, we might make the next step easier on ourselves by having a name behind us.
Either way, good luck.
And, yeah, out of curiosity, nooreen, what's your dilemma?
I don't know, Isidella - I would very seriously consider Mayo. It's an incredible place (I know a guy in the MD/PhD program there).