sorry for the very confusing title... basically I am looking for a yaoi couple in a yuri manga, a yuri couple in a yaoi manga, a homosexual couple in a heterosexual manga. Thank you so so much! To be honest, the only manga/anime I can think of at the moment for this is Mahou Shoujo Madoka, and even that is up for debate... so I guess you can possibly argue that there are some yuri moments in Mahou Shoujo Madoka but also that bit with the green haired girl and Kyousuke...

So what I'm getting is you want a romance.

Inari, konkon, koi iroha GL subplot
Prunus Girl has a yuri as well as yaoi and I think het

There exists the tags "Boy's love as a subplot" and "Girl's love as a subplot"

If you want anime there's quite a few of those...

Seijou Kouchakan no Jijou has both a shoujo-ai and shounen-ai couple/scenes
Tea for Two has a side yuri(?) couple in volume 1,2 & 4 extra
Sumanai!! Masumi-kun has a side (surprise) yuri couple in the story

For anime, I would recommend "From the New World" which as both shounen-ai and shoujo-ai scenes.

Ame Nochi Hare (Bikke) has a GL subplot.

And seconding Shin Sekai yori.

There´s a male character in love with the Protagonist in Mirai Nikki, he even has his own spin off Mirai Nikki: Paradox

Loveless is a shounen-ai manga but has at least one side yuri couple, and some hints at het pairings. It's also one of the best BL titles out there.