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These are example of films that intentionally or otherwise set the religious right (in several different countries) into hissy fits over the inclusion of homosexual themes, characters or content. In some cases, these films were among the first in their market or genre to break taboos concerning the depiction same-sex relationships.
Fire is a 1996 Indian film that was the first Indian film to explicitly portray a homosexual relationship. The two main characters, both in unfulling arranged marriages, turn to each other for support and eventually become lovers and best friends. Hindu fundamentalists and loons in India were on a roll after the film was released. Though the intent of the demonstrations was to shut down the film, in actuality the reverse happen, and a new discourse on homosexuality arose from the ashes of the flame. 
Brokeback Mountain (2005) is about two cowboys who fall in love - with each other. The religious right was not happy with this one becoming a box office hit. One Utah theater chain pulled the film two hours before it was to debut upon learning it was about a same-sex relationship, while Focus on the Family and Concerned Women for America went haywire denouncing it. The religious right's denunciations only served to drum up public curiosity and make it an even bigger success.
Cruising (1980) was a box office hit in which a straight cop (Al Pacino again) goes undercover in the leather/BDSM bar scene to track down a serial killer who is murdering gays, and winds up struggling with his own sexual orientation. The religious right hated this one because of its frank portrayal of homosexuality, one of the first mainstream films to do so. The "mainstream" LGBT activists didn't like it either, and some of the gay community actively protested it, because it focused on the most outré aspects of the leather scene in the manner of an exploitation film (treating it more as a freak show rather than attempting an honest portrayal) and because the serial killer was a gay art student. Controversy aside it was groundbreaking for its time in touching that subject matter at all. While some LGBTs consider the film homophobic, those who were around the NYC leather scene at the time have a more positive view of it as a near-documentary of the leather bars pre-AIDS. YMMV.
ParaNorman is a 2012 stop-motion animated film produced by Laika, it has a sub-plot about Norman's older sister, Courtney, falling in love with a likeable jock named Mitch, who is revealed to be gay in the last five minutes as a gag. Some Christians have even petitioned to change the rating of it to R.
Milk (2009) is a docudrama about the first openly gay person to get elected to the San Francisco board of supervisors, and a cop who ate too many Twinkies. Its release coincided with the California Proposition 8 vote, but its depiction of the 1978 Briggs Amendment being voted down after leading in the polls didn't seem to help Prop 8 meet a similar fate.
The Rocky Horror Picture Show (1975) with its overtly cross-dressing, and bisexual themes. Around this time glam rock brought the first real acceptability of gay identity in rock music (e.g. Bowie, Queen, Mott the Hoople, T-Rex), this film was arguably part of that trend but outlasted the fad to become a midnight cult classic.
Another gay-themed comedy is But I'm a Cheerleader, which follows a young girl sent to a gay re-education camp. Has RuPaul as an ex-gay man.