I agree with DeeLovely79 regarding how a low uGPA could be overcome, but that other things must compensate for it.
Long story short, I'm waitlisted at a decent school (top 30).
I had a fair undergrad GPA, but had bumps along the road.
The ugly: Been on academic probation. Several W's on transcript. GRE scores are average... top 30%, but I realize most admitted candidates are like top 10% LOTRs ranged from generic, vague, or not as helpful (one letter writer said I was top 3 or 4... which is okay, but schools are looking for top 1 or 2...) Things that compensated: Several majors at a good school within four years Dips in grades had explanations, such as how I worked full time while pursuing several masters Professional qualifications - this did not help in two schools (probably because it didn't specialize enough in my field), while it probably helped in the other two schools Disadvantaged background. However, this also did not help much. (I think this helped me get into my undergrad, but definitely not grad)
I'm definitely a mixed / non-traditional candidate. I have no publication experience. My masters degrees were in unrelated fields, so I might look somewhat unfocused. Also, I went the professional route after college for a couple of years.
My biggest disappointment throughout this whole process was how little my masters degrees played a role. I got like a 3.9 in my masters program... and that did not get me anywhere so far. Moreso than not being admitted into a Ph.D. program (so far), this is what gets me the most.