Dear god this is pretty sad how skewed some of this information can be on here. Ryserr thanks for clearing up some stuff.
First off the biggest difference between DO and MD is that the DO's get trained in OMM. This leads to some differences in their boards. The USMLE puts more attention on biochemistry than the COMLEX does. Other than that there is little difference. Many DO schools and MD schools share the same rotation sites so (Mayo Clinic, Cook County etc.) DO's have the same structure as the majority of MD schools; science courses for the first two years and clinical rotations for the second two. DO's have their own residencies that they apply to IN ADDITION to being able to do MD residencies. Most MD residencies in Neurosurgery, Plastics, Orthopaedics, ENT, and Dermatology are filled by MD's however occasionally some will go to DO's. Whether it's because DO's aren't as qualified as the MD's that apply to the program or they prefer to up their chances to match in the DO residencies (which takes place earlier than the MD match and if they match they are automatically withdrawn from the MD match) will be debated till the end of time so don't bother.
I agree people seem to be prejudice to what they don't understand. The bias against DO is incredible on SDN. You would never hear a physician single out one of their collegues simply because they are a DO. In the real world they care much more about the quality of your work than where you went to school. I work in an ER with plenty of physicians, some MD and some DO and I'll tell you right now as far as their ability to practice medicine there is no difference. They are doing the SAME job as the other. If you know any nurses ask them if they are familiar with DO's and if there is a difference in how they practice.
I too applied to MD and DO this time around and I got an acceptance early on from some DO's. This took a tremendous amount of pressure out of the whole process and if you don't mind the initials that follow your name when your a physician I'd recommend it to anyone.
Hope this clears up a few things....
Good luck to everyone in the current or future cycles!