I'm still building my trans related library but liked 'Boys Don't Cry" and yes it was very disturbing. Very well done.
I liked "Bird Cage" too. I don't think they ever came out and called Nathan Lane's character trans (rather than "just" gay) but it seems to me he was definitely trans. I'd be curious to get other's opinion on this.
"Tootsie", while not trans, raised some gender issues for me as he discovered feelings that he had not allowed himself to feel before his "transformation".
"But I'm a Cheerleader" was hilarious and, it seemed to me, right on in it's betrayal of the whole glbt community and its diversity - from glbt persons and their families and the community in which we all must live.
"TransAmerica" will always be special for me since it was the first mainstream movie, that I know of, that dealt with trans issues in a healthy way. Therefor I could order it and not have my wife wonder why I, a supposedly straight husband, would buy such a film. It was later that year that I finally told her I was trans. Yep, it will be one of those special movies for me.
Debbie