The stories on this board are incredible! I am compelled to also share my story as it may give some applicants additional hope.
Like emg28, I am a first generation college graduate. I majored in psychology. I finished undergrad with a 3.0. I had a few failing grades on my transcript (Ds and Fs). I've never been one to make excuses, but I struggled financially, mentally, and emotionally in college due to some serious family health issues.
I attended a school that did not have the best resources to give me the exposure and skills I needed. Realizing this, I sought opportunities elsewhere. I spent two summers as a research intern at two major research universities.
During my senior year I decided to apply to PhD programs in clinical and developmental psychology. Everything I heard from people around me was that students with a degree in psychology go on to get PhDs, so i figured it was what I was supposed to do. I took the GRE and didn't do well at all. The only score I can say I was AW. I had one great letter of recommendation from my research mentor and two average letters from professors in my department. I got rejected from nearly every program I applied to because I did not meet "basic cutoffs". Teachers College rejected me from their PhD program, but accepted me to their masters program. I was completely surprised. I ended up declining the offer though because it did not come with funding, I couldn't find housing, and I could not afford to live in NYC.
A month after graduating, I made the decision to move nearly 2,000 miles away from home and it has been one of the best decisions I have ever made. I landed a job as a research assistant at a major university. The research I have been doing shifted my area of focus and sparked my interest in education policy. I applied to and got accepted to a masters program in public policy. I finished with a 3.9 GPA and made great connections with students and professors. Nearly 5 years after starting as a research assistant, I received several promotions in my current department, lots of great research experience, presentations, and publications. During summer 2012, I decided to apply for PhD programs in Education Policy. I studied my butt off for the GRE and improved my verbal and AW scores, but my already crappy quantitative score actually went down . I was extremely nervous about my chances of being accepted due to my quantitative score and my undergraduate grades, but I took the risk and applied.
Long story short, I am proud to say I got accepted to STANFORD out of over 500+ applicants. My POI and the admissions committee had some questions about my undergraduate GPA and quantitative GRE score, but they gave me a chance to explain it. From what I was told, having a great GPA in a masters program showed a remarkable upward trajectory. Having 4+ years of solid research experience and three glowing letters of recommendation also really worked in my favor. I also did everything I could to try to make myself stand out from the other applicants (a great personal statement and meeting with my POI to discuss research interests). I am still waiting for responses from the other three schools I applied to, but I think getting admitted to my very competitive top choice is remarkable!
I say all of this to say, there are certainly ways you can compensate for having a "low" GPA. Best of luck!