I will be working as an ALT in either Hiroshima or the Kansai area this coming spring. I have been to Japan before and as the only out Lesbian in Nagasaki (that I knew of) it sucked! So since then I have done a TON of research, even took a class at my university called "Queer Japan". So where are all the Japanese queers hiding? Well they are hiding... but once you find someone in the community, it gets much easier after that.
So here are a couple links I will share with you all. If you already know about them, sorry for repeating...
Utopia Asia is a site that is pretty up to date with gay and lesbian bars and queer friendly hotels throughout all of Japan, not just Tokyo. You can even meet people on here and create a profile but there aren't very many members so it's hard to get a reply... but! If we all sign up and post regularly we can change that :3
Out Japan is site that is meant for Japanese and English speakers alike, but alas there are more English speakers than Japanese on here. The plus side is that this site is frequently updated so you can usually get a reply or a friend request within the week instead of within the year.
I also have some specifically lesbian/ bi women websites that are in Japanese. Many of these sites are not as organized as facebook or even out Japan. You don't get a profile or anything, all you can really do is post and from that post you will exchange emails with someone who is interested in you and then decide if you want to exchange numbers, pictures, and eventually meet up. The site I'm posting here is the most updated one that allows people without a Japanese cell phone email to join. There are others that may be better but I can't access them as of now.
Here is a lesbian event I found through one of my groups on mixi...
It's a Christmas party in Tokyo. 12/25/2010 and is rather short, 8pm till 10pm. The exact location is not specified because you have to RSVP at the bottom of the site to get it however they tell you it's at a nice restaurant in Shinjuku. The cost is 4200 yen but it's for a full buffet, wine, Christmas cake and more. The dress code is like dress shoes and nice pants but you have to wear something that has some red or green in it.
So I hope that was helpful information and please feel free to friend me and let me know what your experience has been being queer in Japan :)