From an MD student's perspective, I can tell you this:
IT DOESN'T MATTER.
I'm only an MS2, but from my observation, the 'average' DO is an 'all around' better doctor than the 'average' MD. Thats a sweeping and unfair generalization though; you'll be the doctor you make yourself.
Maybe DOs just try harder to overcome the stigma and end up better. OMM is also awsome stuff, although most DOs don't ever really do it unless it's their specialty or they are in PM&R.
As for schools, I honestly think the biggest difference is that allopathic education may be cheaper and you might have less debt down the road.
MD schools have alot more cash; therefore they have more scholarships. Most state schools are also MD schools = cheaper tuition.
Strangely, MD's on average make a little more than DOs (I think thats a statistical artifact due to more DOs going into primary care and more MDs stroking themselves into g^d-complex specialties.) So maybe these self-absorbed specialists pay off their loans faster. I'm sure there will be plenty of DOs making more in competative specialties than I make as a family doctor, though. Again, you'll be the doctor you make yourself.
So don't stress it. I'd say apply based on where you want to go and how happy you'll be as a student. Some schools are supportive environments (Touro, Einstein, most small state schools) & some are ultra competative & stressfull (Hopkins, NYCOM, Jefferson). The distinction isn't a DO/MD one.
Get in where you can get in. Work hard when you get there. Focus on becoming a great physician. The letters after your name won't matter in 10 years when there are nearly as many DOs as MDs in this country. What will matter is if we can overcome the divisions in our profession and for some class solidarity because the true danger is proletarianization at the hands of Medicare cuts, insurance industrialization, litigation culture, ect.
