If you look at the website for the ranking, it'll tell you what factors they consider and what weighting they apply to each factor.
Factors I've seen used are entry requirements, student satisfaction, staff to student ratio, graduate prospects, number of times the university is quoted in research, money spend per student on centralised services - all sorts of things.
So chek out each ranking and see how the university scores on each factor. Or just ignore the rankings and go there anyway!
The one ranking I would steer clear of is the QS World Ranking, as that's based (to a very significant degree) on a survey they send out to academics and employers around the word. So it's based upon preceived quality, which obviously isn't necessarily the same as actual quality.