MP'05,
I can only comment on my personal experience in this regard. It has never once been an issue that I was a DO for any program. A secretary at Duke told me that they didn't take DO's, and I took her at her word, dropping them off the list. Of course, she was incorrect, as they had DO's in my class there.
I've been at Mayo for four and a half years, having completed my Psych residency, and now working on my fellowship in Psychosomatic Medicine (Consult Psychiatry) here. I also applied for fellowships at Mass General, Brigham & Women's, NIMH, Yale, and the University of Washington, and despite getting interviews at all of them,
not once did my degree come up. It wasn't an issue when I was selected as Chief resident, either. It hasn't affected any of the other DO's in our program, either.
In fact, the last time I was reminded that I was a DO was on a discussion board, reassuring a student. The good news is that once you've graduated med school, the MD/DO issue decreases dramatically.
So the short form (which isn't a means of communication at which I'm very adept, obviously) is that you should apply
wherever you're interested in doing a residency, and don't worry about the DO/MD issue.
I hope this is helpful. Please email me with any questions or concerns,
Chris