Search for potential graduate schools in your field with an online search engine, a graduate program search website such as PhDs.org or USNews.com or in a directory of schools such as "Peterson's Graduate Schools in the U.S."
Narrow your search by region and program size. Most PhD programs require students to be in-residence, or take classes on campus, for at least the first 2 years. Additionally, many programs offer students funding through teaching assistantships. Unless you already live near the college you decide on, you will have to relocate. Decide if you want to attend a university that accepts a large number of graduate students into your department or if you'd prefer a small program.
Rank the following criteria in order of importance to you: research, student graduation rate, student placement post-graduation, diversity, student resources and faculty. Narrow your list of potential schools according to the characteristics that you value most. For example, if you are in a science-related field, you may place more value on the research opportunities at the school than the female-to-male student ratio. Go to each program's website and look up the faculty in your department to give you an idea of the professors' interests and recent publications.
Search for the average GRE scores for accepted students in each of the programs still on your list. Compare to your scores if you've already taken the test or your expected scores if you haven't. Be realistic. Look up the average GPA of the incoming students and compare to your own. Rank the programs where admission is a long shot as "Reach" schools, those where it could go either way as "50/50" schools and those for which you more easily meet the acceptance criteria as "Safety" schools. Remember that schools consider all components of your application, not just your GRE scores and GPA.
Consider tuition and available funding. Many PhD programs provide partial to full funding for students. Additionally, financial aid is available in the form of student loans, and there are many competitive external funding sources. While the potential debt you incur for graduate school in the form of tuition and fees should play into the ranking to a degree, this should be one of the lower criteria as funding is often available for PhD candidates and many schools are willing to work with students to find a way to finance their education.