Ran + Aya
Ran (aka Aya) has a little sister named Aya. When Aya was sixteen, she was hit by a car (order given by Reiji Takatori) and went into a deep coma. (FYI – She stayed in the Magic Bus Hospital). Ran wanted revenge on the Takatori family for hurting his sister, so he joined Weiss and planned to assassinate Reiji. He took Aya’s name and put on her earring in order to “be” Aya until she awoke (yeah so much like Nuriko from Fushigi Yuugi right?), and most people (including Sakura Tomoe and Omi at first) thought that maybe Aya was Ran’s lover, since he was so close to her and visited her so often, but in reality, Aya was Ran’s beloved younger sister.
Omi + Ouka
Ouka originally has a crush on Omi, and visits him at the flower shop a lot. When they finally do become a couple, Ouka learns from Shwarz that Omi is actually Ouka’s sister (yup it was incest) because they both came from the same father (Reiji Takatori) so Omi says he’s happy that they could at least be siblings since he was always alone he was happy that he had a family now. When Ouka agrees, she’s killed by Shwarz and that’s the end of that “relationship”. (FYI – Later we learn that Omi’s father isn’t Reiji Takatori, but his brother Shuuichi Takatori is his father so they’re not brother/sister, but cousins.)
Nagi + Tot
Now this is an interesting relationship…enemies in love. Nagi falls in love with Tot, even though she is an enemy of Shwarz, and he is always trying to protect her. It is said that Nagi falls in love with Tot because she is like a pure image of a child (and his childhood was pretty screwed up). When Tot is killed by Farfarello, he totally looses control and destroys himself and everything around him using his telekinesis (rumoured that his powers are amplified when he shows emotion because he hardly ever does…), but after everyone is gone, Tot rises from the rubble (yup she’s still alive), and Nagi makes an appearance at the end of the series (without Tot) where we assumed he was killed. In the ending of the series, it shows Tot alone in the field where Nagi and Tot “fell in love” alone and she stares into the forest where Nagi first approached her. Sometimes I question whether or not Tot shares Nagi’s feelings because she doesn’t seem to commited to him, but she does say that she wants to live with him after they get their revenge on Weiss.