They also reveal that while Hojo may have always had some Jerkass tendencies, he genuinely loved Lucrecia and was devastated by her apparent death.
The Bar scene in Chapter 27. In the middle of all the craziness happening around them, Zack, Vincent, and Sephiroth manage to find the time to go out for beer and hot wings to blow off steam.
The Undying Loyalty Sephiroth inspires in the SOLDIER operatives under his command can be genuinely uplifting. When planning his defection from Shinra, he goes to each of his men and tells them about the Jenova cells placed into their bloodstream mean that they're basically conditioned to follow his orders no matter what, and that he will not force any of them to come with him against their will. Every single SOLDIER insists that they're Not Brainwashed and pledge him to the ends of the earth and beyond.
Genesis and Sephiroth's reunion in Chapter 42 and the You Are Better Than You Think You Are speech that follows. Even when Genesis is angrily demanding a confrontation, Sephiroth refuses to fight his friend and tells him that if his blood can cure the degredation then he will gladly offer as much as Genesis needs.
When Sephiroth meets his younger brothers (the Remnants from Advent Children) for the first time , the three of them quickly tackle him in a group hug. The whole scene is so adorable that despite his lack of social skills to tell him what to do in this situation, Sephiroth can't resist giving Katagi (Kadaj) an Affectionate Gesture to the Head. And despite having only just met them and only knowing of them through Shinra files, Sephiroth immediately accepts them as family (which they technically are, since they were born in-vitro using both Hojo and Lucrecia's DNA).
Once they've been smuggled out of Midgar, one of Palmer's daughters gladly agrees to take care of them in Kalm.
Scarlet smuggling them out of Hojo's lab is a combination of heartwarming and awesome.
Sephiroth goes through Hojo's wallet after Vincent kills him., he finds laminated photos of himself at various points throughout his life, along with Hojo and Lucrecia's wedding photos. He also finds a note written to him on the back of the wedding photo telling him not to forget his family (referring to his brothers (The Remnants), and his cousins (Rosso, Nero, and Weiss)), telling him that his mother has the key. While not clear, it seems that even being possessed by Jenova and having undergone years of Jenova-induced Sanity Slippage, he still loved his son and managed to regain his senses long enough to leave Sephiroth a clue to help him free the Tsviets from the leash of the Restrictors.
Sephiroth attempts to commit suicide in Chapter 59 to help destroy Jenova, but because of the Jenova cells in his body, he's able to have a psychic conversation with his real mother for the very first time. Tears of joy ensue for the audience.
When Aeris' healing rain starts to kill Sephiroth, Genesis, and the Tsviets, everyone immediately drops what they're doing to help them. In order to save their friends' lives, the heroes plant summon materia in the wounded warriors' chests, like Lucrecia did with Vincent. And it works.
Once the battle is over, Zack proposes to Aeris right there on the spot.