In addition to the awesome resources of NIH and living in DC for a year, about half of the NIH scholars get a scholarship covering the cost of your remaining years of medical school. If you're at a private school, this can be a hefty sum of money.
I thought it was just the Howard Hughes Cloisters program at NIH that pays for your remaining years of school. Does CRTP really offer that as well?
I have known friends that have done both Doris Duke and CRTP. I don't think you can make a bad decision either way. I do think that for certain individuals that one program is better than the other and this depends on the field into which you are planning to match and also your goals and motivations for doing a year of research.
For example, my field is radiaton oncology and doing a Doris Duke year at either UCSF, Wash U, or Harvard would help boost one's chances for matching more so than the CRTP. For most fields, I imagine that this is not the case, and that the CRTP would be the better choice.
As for prestige, I think that is hard to say. The CRTP benefits from its NIH ties and from the incorrect assumption that CRTP is the same thing as the Howard Hughes NIH cloisters program (basic science researh year, not clinincal research). That is not meant as a slam against the CRTP, as it is a great program in its own right.
If you care to share more info about your field and what you are hoping to get out your reseach year, then all of us could give more helpful and accurate advice. BTW, there are no right or wrong reasons as to what you are hoping to get out of the year. Many people want to maximize their chances for residency, some just want a break, others want to be near a significant other, some want a high powered research experiences, and some just want to have fun.
-XRT