You pick those that stand out or are unique. Being male in the applicant pool makes a person unique. I am not saying that a "less qualified" male would get in over a female in the 90% pool you mention.
For instance if you were comparing 2 applicants thet were well qualified and hypothetically speaking say they had the exact same GPA, GRE, oh heck say they have everything the same, except one is male, the other is female, and there is only one spot left in the class. I would say that the male would get the seet and the female would get alternate listed.
And of course schools will not put anything in writting about giving a preference for a certain gender....but many schools say they "seek to diversify" there classes. Diversity has a lot of different aspects, gender being one. Also in my application process, I have actually heard schools admit that they need male applicants.
There's the longer version of my 2 cents.