Safer sex information, resources, and outreach. Trans-friendly in general, and has been doing outreach specifically to the FTM community to find out what they can do for us.
BiNet, like many bisexual organizations, has a strong alliance with the transgender community. Most recently, they withdrew their support of ENDA when other lobbyists refused to use trans-inclusive language in the employment non-discrimination act.
GLAAD has never let its name stop it; it has a long history of bi and trans inclusion, and has been reporting media transphobia in its weekly "GLAADAlerts" for years.
The NCLR provides free information and counselling to lesbians, gay men, and bisexual and transgendered individuals, and technical assistance to attorneys. One of their two staff attorneys is an FTM activist who has done extensive work with city and legal groups, and the HRC, to bring transgender rights to the fore.
They really mean it - youthresource.com has a series of trans feature articles, perspectives from trans youth, a study of trans-youth-specific health risks, and a trans youth webring.
NGLTF refused to support ENDA unless it included transgendered people, and did a study with GenderPAC which found that "28% of Gay, Lesbian, and Bisexual people have been discriminated against based in part on their 'gender expression.'"
Support and advocacy organization for children of lesbian, gay, bisexual and transgender parents. They have considerable support for transgendered parents and children, including hosting trans-specific gatherings.
NYAC has been working on outreach to trans youth for several years, and has transgendered folks on its board of directors.
It's a magazine! it's an activist organization! you're both right! Anything That Moves has put out full-page ads with the bi and trans counterarguments to the "ex-gay" issue. Every single issue has transgender content, and they don't even require that it be bi-focused. Even their ongoing soap opera installments have a recurring FTM hunk.
PFLAG (Parents Families and Friends of Lesbians and Gays) is a national organization promoting the health and well-being of gay, lesbian, bisexual and transgendered persons and their families and friends. They have a trans-specific chapter (PFLAG-TSON) and several pamphlets on subjects like "Our Transgendered Children."