In the manga version of Elfen Lied, Nyu's love of breast squeezing is taken far into Les Yay territory with both Yuka and Nozomi. Were it not for a timely intervention by Kouta, she might have actually raped Nozomi.
At one point, Yuka and Nozomi actually got aroused from it.
... and with Mayu: In the anime, Nyu gropes/washes her in the bath and it seems to not be a wholy unpleasant experience. In the manga, however, Mayu reacts much more negatively. Nyu is able to understand at least that much, is slightly perplexed and saddened, and any further Les Yay there is put to an end.
Nyu has the mind of a two-year-old inside the body of a teenage girl and has no inhibitions about her libido. Which makes it more than a bit Squicky.
And later in the manga, after being Nyu for a long time, Lucy at one point looks at Yuka and is puzzled why she is feeling compelled to grope her.
Also, there must be some chemistry between Mayu and Nana, considering how much fanwork there is of them.
Also Nyu and Nana, which is somewhat Foe Yay due to Nana's feelings for the "Lucy" personality.
In the manga's very last chapter, we have Anna Kakuzawa and the Agent.
Then there's Aiko Takada from Chapter 85 and the OVA. She seemed to have quite the crush on Kaede and wanted her to model for her drawings. Later, in the warehouse, she says that she wants the two of them to be together forever, and even kisses her (on the cheek) in the OVA. Of course, since she was such a minor character and died so shortly after her introduction, this one is easy to overlook. But Lucy's grief over Aiko's death was what drove her into her vendetta against Kurama, so she obviously had feelings for Aiko as well.