This was a really difficult choice, I have to say. I have a certain type of personality that I like in my yaoi couples, and thus when I find it, it inevitably ends up in my "Favourite" list. However, even there are some more special then others, and this is one of them: Sakisaka Shou and Hirose Takashi from manga "The Other Side of You".
As you can see, this manga is a little older, but from the time I found it, I read it about seven times already, and mean to reread it again in the future. The story, while using an already used idea, manages to be a unique one too: Takashi and Shou are childhood friends, and a very good ones to boot, until Shou's parents decide to divorce and Shou has to move far, far away. Takashi is devastated, but promises to write and call, and fulfills his promise diligently... Only Shou doesn't write back, and refuses to accept his calls. What is going on? As fate would have it, independently of each other they decide to go to the same high school, where the story starts. Bad things happened in Takashi's life, but his personality stayed the same, kind, optimistic and above all, persistent. Even after Shou repeatedly tells him he wants nothing to do with him, he doesn't give up, wanting their old friendship back. When Shou decides to leave, that is, run away, again, Takashi's stubbornness makes him reveal the reason for all this avoiding. Which is totally predictable, of course. But the story doesn't end here. While Takashi doesn't know whether he loves Shou back, he knows he doesn't want to part again, even if it means becoming lovers. One of the things that made this book really refreshing is that personality of his, naive while deeply aware. He knows what he wants and doesn't let anything to stop him. Insecure Shou doesn't stand a chance :P The whole book (two, in fact) is quite realistically written (drawn?), with Shou's past being hurtful as well, Shou's girl friend (but not girlfriend) acting the way she is, the reaction of the school when they discover their relationship, Takashi's father disinheriting him (in a way, this was one of the funniest parts for me)... As it is said in the end, the relationship wouldn't have a chance if Takashi wasn't the way he is. I always wished I could be more like him, direct to the point of painful. And hitting Shou in the epilogue was definitely the right thing to do.
So if you are looking for a philosophical manga with a plot, with believable characters and realistic setting (and happy ending, of course!), this is the one for you. You definitely won't regret.