Hi,
I had earned a Masters before I applied to PhD programs. My BS was in Forensic Science (basically I did everything "Pre Med" students did except physics plus I got to take really interesting bio-science based Major classes), MA in Anthropology. My GPA in Undergrad was ok but in my MA it was much higher. Anthro programs at the PhD level rejected me all 3 times I applied (including this one) but I tried another approrach to a non-anthropology program but that is a much better fit for my research and personal interests/goals and I just got accepted this week!
I think the big take-away message is to find a good fit. People told me this everytime I applied but I don't think I really understood what that meant until I actually DID find a program where I would "fit". I have always been worried about GRE scores, not having the same research experiences as other applicants, etc but I really think that this time I was more focused on the important point: Will I be a good fit? This program is geared toward graduating people who can teach AND be excellent researchers. I've done research through my Masters and I've been an adjunct at the university and community college level for 4 years now. Combined with my research goals and relationships with potential advisors that I've been building to find a good place to fit in the program, I think that helped. In fact, they even told me that the Masters was a plus because that tells them that, at least, I know how to do research at a basic level.
It's a rough road and once you get in it will be another set of challenges and opportunities! I'm excited!
I wish you luck!