Great topic! Don't have a lot of time to chime in right now, but two titles that immediately come to mind are Au hasard Balthazar, directed by Robert Bresson, and Unsere Afrikareise, directed by Peter Kubelka. Both were made in 1966, and both are cinematic masterpieces. Both films deal, in their different ways, with the theme of human cruelty to non-human animals, and are really eye-openers on that score.
Another great film worthy of mention is Beau travail, a 1999 feature directed by Claire Denis. An updating of Herman Melville's Billy Budd, this beautiful film shows, like in Brokeback Mountain, how repressed homosexual desire can poison and destroy the lives of men. One of the last great films of the twentieth century, and one of the best gay-themed films I have seen.
Cheers,
Scott