Kemetic Orthodoxy is very LGBT-friendly; it married a pair of gay men years before it was technically legal in the state where it happened (Illinois), several of the priests have been bi, lesbian or gay, at least one was asexual, and there were a handful of openly trans* people around.
Wicca is mixed – mostly positive overall, but some groups have gender role hangups and at least one is obnoxiously transphobic (in the guise of being feminist). On the other hand, there’s at least one radical gay activist Wiccan group.
Most other pagan groups tend to be pretty relaxed about it as far as I’ve seen. I don’t know what cultural biases might exist with Taoism and Shinto, but at least what I’ve read on them doesn’t indicate any bias against homosexuality or gender diversity.
