I would disagree with njbmd and suggest that "Applying disadvantaged does not affect your application other than in a statistical manner. The AMCAS can use your status for generating statistics." may be true for his school, but not every school. Still, I don't know this for certain, and I've been unable to become a student adcom myself. Still, I think it's silly to say "who shows promise of being able to complete our curriculum". How many students fail out of your school anyway? Does it correlate nicely with GPA and MCAT scores before they started? (Psst, I already know the answer to this nationally. It doesn't.)
I applied as disadvantaged, and most people do tell me I was very justified in doing so. It's hard to say whether specifically checking the disadvantaged box and writing the disadvantaged essay meant anything, but the topics I discussed in my personal statement and disadvantaged essay came up in almost every interview. Many wanted to see if it was true, others wondered how it was possible.
It's true that many people who interviewed me paid little attention to my application. I did end up getting accepted at one school where they admitted they usually didn't even read things like personal statements. Still, at my second interview, my interviewer was so impressed with my essays and my interview that they offered me a rare early acceptance.
I encourage pre-meds who have a unique and challenging background to apply disadvantaged for whatever it's worth. Some adcoms do appreciate diverse backgrounds among their students. The vast majority of pre-meds come from middle to upper class families and as a result medical school classes feel homogenous. It irks some of us, including some adcoms. If some adcom somewhere is trying to produce the future leaders of medicine by selecting those who have come from a place that gives them the drive to do something about the problems in medicine, kudos to them. That's how I got into Penn when all the other top-10 schools rejected me. The adcom who selected my application brought me in to interview with him. He told me "I wouldn't have interviewed you, but I wanted to see if your application was real." Had my application been reviewed by with a different adcom, it's likely I wouldn't be here.