In 2006, the AP Stylebook, the most widely used by journalists and editors, was updated to include usage standards for terms related to transgender people. The AP Stylebook encourages writers to "use the pronoun preferred by the individuals who have acquired the physical characteristics of the opposite sex or present themselves in a way that does not correspond with their sex at birth."
"If that preference is not expressed," the Stylebook continues, "Use the pronoun consistent with the way the individuals live publicly.
New York Times Style Guide
According the New York Times, About.com's parent company, transgender "is an overall term for people whose current identity differs from their sex at birth, whether or not they have changed their biological characteristics. Cite a person’s transgender status only when it is pertinent and its pertinence is clear to the reader. Unless a former name is newsworthy or pertinent, use the name and pronouns (he, his, she, her, hers) preferred by the transgender person. If no preference is known, use the pronouns consistent with the way the subject lives publicly."
Read more about proper transgender terms in Is It Okay To Use The Word Tranny?