I'm kinda surprised Hana Kimi isn't mentioned yet :D There was one gay guy who was in love with Nanba-senpai, though it was portrayed in a comic manner, so if you're looking for a seriously portrayed relationship, that doesn't fit.
Love Shuffle was already mentioned, but sadly, the fact that one of the characters is gay, is actually a spoiler, and rather important one...
And then there's Japanese movie called Boys Love, the main plot line is about two gay guys struggling with a relationship. And it's pretty much not explicit to be shocking, it has only one or two sex scenes, and the most you can see is a naked butt.
[That's it from the ones I watched]