Coming late to the conversation, and it looks like all the ones I'd recommend have already been recommended, except perhaps Antonia's Line, which isn't so much a specifically lesbian film as it has a storyline in it.
There's also Fire, and Aimee and Jaguar, Hours, Love My Life, Ma Vie En Rose, and Transamerica. There was also an episode of The Listener that had a trans theme, but I'm not sure I'd list it as good.
On a side note, Dirty Martini is onscreen in the background for like, 3 seconds in one of the club scenes in Short Bus, which is a nifty little flick, though not lesbian focused. That made me several shades of happy :>