I am an applicant for this year.
When was looking for schools to apply to, I looked at field rankings on RePEc to find departments/people I was interested in, then ranked those by what I felt was the best fit. I then looked at the USNews, Tilburg, and RePEC department rankings as a whole to get an idea of where they fell and which I could cross off my list because they were either unattainable or nearly unranked.
While I applied to schools ranked between 15-60ish, my personal preference is dictated mostly by what I perceive to be a good fit, and "ties" are broken by overall ranking.
I'm sure other people have better systems, though.