I like I Can't Think Straight. It's probably the major popular lesbian film ever made. I also like Imagine Me and You, and D.E.B.S. D.E.B.S is more of a teen film. Sorry these are all lesbian films… I don't know many others…
I have to agree that Rent is my favourite. I haven't had enough exposure to LGBT movies yet, I have to really on the tiny bit of exposure we get in the mainstream (Dumbledore anybody?) But in terms of musicals, I think all of them could realistically be classed as LGBT. But Rent and Avenue Q are the only ones I can think of off the top of my head with major LGBT themes.
"Aren't all musicals gay?" - Roy (IT Crowd) Avenue Q is definitely the only musical I think I've seen with any serious gay vibe to it, and it was fantastic...