For me, ultimately it boiled down to fit and prestige of the school. It really helps if you get a chance to visit the department/campus. Some miscellaneous aspects also affected my decision.
School A was a perfect fit, intellectually speaking. My potential advisor is a top person in the field. The campus is beautiful (its right on the beach) and the city is even more so. The grad students are really cool and easygoing.
However, despite the decent package they offered me, I was concerned with the high cost of living and relocating more than 3000 miles away from my home town/state ( what would I do with my stuff?). Also, funding opportunities for the summer are very competitive and perhaps unavailable to me the first two years.
School B offered me a bit more financially, and the cost of living in the city was so much lower than in school A. Also, they told me that the department has money to go around, so if I applied to a summer grant I would probably get it. Plus, I would not be so far away from home.
However, it was not a good fit. I did not connect with my potential advisor in any way, shape or form ( I felt like perhaps she did not even thoroughly review my file). I did not like the campus much, and I really hated the city.
While my wife and I may be broke for the next 6 years, I chose school A and am really happy with my decision. Now I just have to finish my Masters ( I am running out of gas), pack all of my crap and drive across the country.