Hi-- I applied this application season to 15 schools, ranked from one to 30 something on the Leiter report, and was grateful to be accepted to a few of them. One thing that I think helped was that the professor who gave me my lowest grade addressed this in his letter of recommendation. He explained that the grade was in a graduate level course, I worked very hard, did well on final, etc etc.
I did not have the option to re-take the class, as my school only allows grades to be replaced if the grade is below a c-. (A terrible rule, in my opinion! What about the people who want to replace a B+! or a C!) Okay, my point is that I think it could be helpful to retake that class if you can, and if not, to see if at least one of your letter-writers might comment on that. It was one thing to give my own explanations in my statement of purpose, but I think it helps to have a respected philosopher agree with you.
One more note of advice: a student I graduated with also applied to many schools, had a fairly similar GPA to mine, and above average , although not stellar, GRE scores. I believe that his writing sample was strong as well. In any case, the student was rejected everywhere that s/he applied, and after a lot of research into the reasons, it became clear that the letters of recommendation were not very strong. For one of the letters, the student asked the super star professor in the department, although he had never even taken a class with him. It was probably clear to that professor that the student just wanted to use the big name of the professor, and the professor wrote a letter that basically said "I am not familiar enough with the work of this student to make an accurate judgment." This is then very questionable in the eyes of admissions departments, because it makes the student appear shallow, and it also raises the question of why the student didn't get to know any other professors well enough to ask for a letter.
So, if you are searching for your other two letter writers, look for people that know you well and know your work well. If you happen to know one of the superstars from your department well enough to ask for a letter, that is a double bonus.
and I second the above advice to apply widely. It is insanely competitive-- more so than I thought it would be. I had a 3.9 phil GPA, 3.8 overall, over a 1450 combined GRE with a solid 6.0 on the writing section,and my writing sample paper earned me high honors. Yet none of the top thirteen schools even put me on a waiting list. I did not really expect it, and I am not trying to say that my stats are particularly impressive, I just want to say that when I applied, I was under the impression that I was in pretty good shape. Other students that I know who had more impressive stats, such as a published paper as a writing sample, still had trouble getting into top ten schools. Luckily you still have time to research schools and see where to apply In a way, I enjoyed the whole process, so I wish you luck along the way.