My most important factors are very different than a more traditional student.
In order prior to applying:
Location--must be within an hour and a half of either my family or my husband's family. After doing undergrad and an MS without anyone we knew around, and wanting more children which will have to happen during the phd program due to my age, we need the support of family as backup childcare.
Location--must be within thirty minutes of a branch of my husbands company so he can transfer his job to a new location same job/benefits
Location--must have a private Montessori school for my daughter
Research--must have X-ray crystallography equipment and / or protein structure labs that utilize NMR for structural elucidation
Funding--my current school is very short on funding and the limits on graduating on time simply due to lack of money is not something I want to deal with again
(Thankfully both our families are in metropolitan areas with a vast array of schools in the top 100 for my field)
Those were factors for where to apply. Since I only applied to schools that fit that criteria, my factors for deciding in order are:
Lab and school culture--will my PI be okay with me needing to leave if my kid gets sick and okay with me coming in super early (4-5 am) to leave by four thirty - five instead of what a lot of people do which is roll in around noon and work til 8 (at least in the phd program at my current school that's what everyone does)? Is the school environment supportive of families? Will I lose stipend if I take six week maternity leave later into the program?
Research--how many potential PIs would I have? For example: At Ga Tech there are only two I would want to work for. At UNC Chapel hill, I can list 12 of the top of my head.
And that's about it for me.