As an MD/PhD candidate from a top 10 medical school who only applied to one residency program, my situation is somewhat unique and may not be broadly applicable. What I can say about my residency application process is that I gained important perspectives on how residency program directors think, how to optimize your application, and even how to negotiate the process (you can negotiate more than you think!).
One of the major reasons it worked out so nicely is that I decided to apply to a less competitive specialty. I wasn’t sure exactly what specialty to apply to until I was well into my PhD, and in fact I had briefly considered other “alternative” career paths. Eventually, my PhD work began to solidify and I started making really cool discoveries, and everything finally came together. I wanted to keep up the hot streak, so to speak. In terms of my overall career goals I knew that staying at Duke would be best for me given the strength of my current research environment. Therefore, I set about determining which specialty might give me the most research flexibility during my residency and fellowship training. Pathology it was. Also, how cool is it that technology is getting so advanced that you can actually practice telepathy?! As a side note, I will say that my MD/PhD colleagues applying to Rad/Onc, Neurosurgery, or even Internal Medicine apply more broadly and may have slightly less control over where they ultimately end up.
Over the course of several discussions with the program leadership, we decided on the best way to structure the residency and fellowship time and how to integrate dedicated research time. For these discussions, knowing what you bring to the table, knowing what institutional initiatives are available (eg. will the institution provide funding for a technician?) and what the regulations are of the certification board (in my case, the American Board of Pathology) in order to meet criteria for board certification was important. In other words, do your homework. In the end, my advice would be to really take the time to reflect on what career path might be best for you given your unique situation (I cannot stress the importance of actually talking with people who are in the field!). If you play to your strengths, the residency application cycle may not be as daunting as it seems.