Transgender/third gender/nonbinary people are a minority that has at times been marginalized within the LGBT community. The good news is that people who fall under (or near!) the transgender umbrella are increasing in visibility; more and more, their rights are part of discussions by the broader public. For resources, see LGBT Rights in the Workplace (courtesy of Brandeis University).
There are many sources of support for people who are gender nonconforming.
at Northeastern University
to connect with the local LGBTQA community.
Gender Spectrum-- support for families of gender nonconforming children
Transitioning when you're nonbinary-- from Micah's Neutrois Nonsense blog