(tongue in cheek) I object to the characterization of females as the fairer sex...they don't have modifiers to Cha (and thus are not more attractive) or Wisdom, (and thus are not more objective and unbiased).
Well, you can make a pretty good case that the Aes Sedai are in charge of the world in d20 Wheel of Time, and a pretty good case that they're good guys (or no worse than Lawful Neutral) for the most part.
Haven't you heard the reason that married men make better soldiers? They're used to following orders.
(that's a joke for us married guys out there...)
But, I assume you mean by "in charge" as in control of most aspects of society - government, religion, military, financial?
I'm sure there are some that have been published - Kalamar has a nation called "The Queendom of Tharggy" where women run all aspects of life, but that was due to a huge war where their men fought basically to the last men and women took up leadership roles out of necessity, and it has stayed that way - but, my collection of non-Wizards of the Coast d20 product is extremely limited.