In my experience, the best GLBT publishers are the smaller, more intimate publishers. They do not pay as much, but their workmanship is top-notch and high-quality, not to mention there is a sense of family. Their work is very well thought-out, and they connect with their authors on a more personal level. I prefer connection over cash, and I sleep better at night knowing that my book is in good hands with people I trust rather than an editor I've never spoken to. The ones I would recommend are Silver Publishing, eXtasy Books, and Dreamspinner Press. I would also suggest trying out some mainstream publishers such as Samhain Publishing or Carina Press, which is a subsidiary of Harlequin Romance. There are plenty of others out there and a lot more options especially if you are looking for publishing in print rather than in e-book format, but these are the ones I've had the most positive experiences with.
Silver Publishing is a company that is rather well-known, some people have heard the name in passing. It is a publisher that gives fair nods to either homosexual or heterosexual novels. The publisher does not discriminate against a manuscript based on the fact that it is either homosexual or heterosexual. The publisher views both as equals and accept manuscripts based on quality, not so much on whether it is gay, straight or a mixture of the two. They are called 'the publisher with a difference' and they truly are.eXtasy books is a small e-publishing company that works with anything from science fiction manuscripts to transgender coming-of-age stories. They have a very broad spectrum, and they also have a very dedicated, tight-knit staff and a network of authors that are more like family than anything else. Their editor-in-chief and acquisitions editor are both incredibly nice and helm a very efficient staff that get the job done right. They accept gay, straight, bisexual, and transgender manuscripts. Again, like Silver Publishing, they do not discriminate based on the sexual orientation of the characters.
I have had less experience with Dreamspinner Press, Samhain Publishing and Carina Press, but I have also heard that they are fantastic options for an GLBT manuscript. Dreamspinner Press was recommended to me by a great writer, and I trust her word as an author. They are also moderately well-known for GLBT manuscripts.
Carina Press is a digital-print subsidiary of a larger romance publisher, and it allows the parent publisher to branch out and publish a different kind of manuscript, and that means GLBT manuscripts. Their slogan is 'where no great story goes untold' and they strive to make sure the stories that need to be heard are. Samhain Publishing has both a Romance line and a Horror line, and they do not discriminate based on sexual orientation either.
Those are the best GLBT publishers in my experience as a published author. I prefer smaller but more passionate workers over a big paycheck and an impersonal process. Part of publishing a book is putting your heart into it all over again, and these publishers assist in recreating that.