These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Between Kakeru and Liselotte. In a SS, he even had a H-scene with her. There is also between Avaritia and Liselotte in the OVA.
Kanae and Shuu in Crossover. She has apparently a kind of attraction toward him.
And a bit between Misao and Scholastica too. According to the Phantasmagoria spell, it seemed Misao was actually the person who Scholastica cared the most about. And Misao lost it when Scholastica is killed.
Ho Yay: Between Georgius and Samson in Before Story arc in Resona forma even if Samson actually loved Misao .
Yukiko enjoys to touch the breasts of the others girls. Kukuri and Yuka are even confused about it. The OVA had Yukiko nibbling on Yuka's ear and giving her a deep kiss. Yuka's facial expression? It seemed like she liked it! She is also often showed in Les Yay position with others girls 11eyes in official arts.
Between Mio and Shione in the Crossover story. Mio wants to protect Shione more than anything and would like her happiness.
The anime version of Yuka crosses it when she tries to kill Misuzu with a razor blade in her tea, which doesn't happen in the original game.
In Before story it implied Invidia crossed the line as she killed a man who had a different belief of her and even if she was sent in mission by Index, it didn't prevent her to take delight to kill him. Without forgetting she also tried to kill Misao for nearly the same reason.
Rescued Fromthe Scrappy Heap: Yuka Minase to a certain degree for her anime portrayal (depending on who you ask). The middle episodes brought to light her Bitch in Sheep's Clothing persona, but episode 12 attempted to calm the past viewer hate with a Tear Jerker flashback that showed the childhood memories between Kakeru and Yuka.
When Yukiko killed Takahisa, as much in the game than in the anime.
It kinda applied to the episode 12, where Kakeru reminisced his past with Yuka which shows how she always supported him during their childhood and after the death of Kukuri. However, it could be subverted as Yuka had been showed as a Bitch in Sheep's Clothing during all the half of the anime.
Lisette's past without any doubt.
If story. The moment where Verard saved Lisette, then died after having fought 90,000 crusaders for her safety will make you cry like a baby. Especially the scene where Lisette confessed her love and answered his name, Verard disappears and returns in his time before to be killed. He understood his death now has a meaning.
It's a lot sadder when you realized that If Story is just a fictive story made for fans. So, this story didn't really happen and Verard didn't really save Lisette.
Before Story without any doubts has a lot of Tear Jerker moment, as the story told the past of the Black Knights. If you played the original, you'll expect what's happened to them.
Every deaths of the Black Knights will make you cry. Especially Irene's and Sebastianus's deaths when we understood that Irene was apparently pregnant, so their happy ending fell.
Samson's death. Especially when we learnt that he loved Misao from the beginning and didn't hesitate to sacrifice himself for her safe.
Even if Benedictus wasn't really a sympathetic character, you'll feel bad for him as it's the only moment where he actually cared and cried over someone, making him slowly Jerkass to Jerk with a Heart of Gold.
Liselotte's defeat. Subverted in the anime.
The Scrappy: Yuka Minase's portrayal in the anime compared to her game and manga counterparts really ups her Yandere, Clingy Jealous Girl, and Bitch in Sheep's Clothing tendencies towards Kakeru; causing a lot of viewers to despise her as the anime went on. The low point was passing the Moral Event Horizon when she attempts murder by putting a razor-blade in Misuzu's tea in episode ten.