Komatta Toki Ni Wa Hoshi Ni Kike!
The most ambiguous relationship in all shounen ai I've read so far, I know that Shounen Ai tends to be like that. It's frustrating to have to interpret their relationship yourself, but I really love this manga. Kiyomine was a bit of slutty jerk though. I can totally imagine Kiyomine having multiple sex partners, and then getting mad at Takara when he find himself a girlfriend.
Rutta To Kodama
Wish they really did switch roles sometime!
Torikago Syndrome
The problem with shounen ai and dark/psychological manga is that there're a lot of hints or suggestive scenes, but you can't be sure what happened. For example, the incestuous relationship between Kain and his mom or his twin brother, Litch. There was scenes that would suggest Kain's mom had sex with him because his shirt were opened, but maybe she abused her son in non-sexual way. Yaoi would give more impact to this kind of tragic story, make the scene seems clearer without interpretation by the reader, like Acid Town, which obviously indicated the rape really took place, or the relationship between the twins.
Yume wo Miru Hima mo Nai