Matthew Shepard Resources Online, via John Aravosis's Wired Strategies page. He is a DC-based lawyer/lobbyist who has kept us abreast of the latest news concerning this case. It's good for the latest and is a good archive as well.
The Advocate: The oldest national gay magazine, and according to Guiness World Book of Records, one of the most bought. Not perfect, too glossy, and a bit more mainstream for my tastes, but, I am still glad it's there. Sort of like the flag.
Anti-Violence Project: This is our local (New York City) Gay and Lesbian anti-violence project. It's not a perfect site, but it does have some of the latest info on homophobic incidents in the city, and some safety tips as well. It is not updated nearly as often as it should be.
Gay City News This weekly gay newspaper is based in NYC but has a nationwide readership. You can sign up for email alerts. Plus, I write for it. Gay City News is the successor of LGNY.
Gay and Lesbian Alliance Against Defamation: A nationwide organization devoted to promoting positive LGBT images in the media, and protesting the negative ones. I like knowing what's happening out there, but I am not too thrilled to hear that GLAAD has accepted money from the ultraright-wing Joseph Coors Foundation.
TurnOut! is a homepage by a Lawrence, Kansas resident who chronicles gay rights issues as a subset of his mainpage, Turn Left: The Home of Liberalism on the Left. I don't know how he does it all. This is a good resource for politics and activism.
Yahoo's Full Coverage of Gay and Lesbian News: Get the latest headlines in LGBT news from a variety of of local and national news sources, from AP and Reuters down to local press, worldwide.