It's only alluded to by the man himself and certain documents you find throughout the game but Pagan's affair with Ishwari Ghale is a massive one. While it initially started out as a simple deception, it grew into true love with Ishwari bringing out the best in him, up till that point a utterly irredeemable madman and making him genuinely happy for the first time in his life.
Another one from Pagan the ending if you let him live. You've been fighting this guy's army the entire game and when he's confronted, he still genuinely cares for Ajay and takes him to his half sister's shrine to place his mother's ashes. Then Pagan, before going into exile, names Ajay as the heir of Kyrat. His only retaliation? Stealing Ajay's helicopter.
If you lean to the Noble Demon side of Pagan Min's characterization, this quote counts.
Pagan: You know, the first and only I time I entered this place, I entered a sane man, and came out like this. But you, you will come out a king.
On a similar note is the secret ending. If you don't go investigating at the start of the game then Pagan returns to the dining room and acts as the perfect gentleman, kindly leading Ajay to the shrine so he can set his mother's ashes to rest. With that done, he leads Ajay to the chopper and offers him a chance to "shoot some goddamn guns" like a cool father figure.
While also a Tear Jerker the player has the option of not killing Dr. Noore. It doesn't save her from suicide, but during that scene Ajay tries to talk her out of it.
If you take a moment to consider, Ajay manages to keep his mother's ashes this entire time and never forget his mission to bring her ashes to their final resting place. It becomes doubly heartwarming if he lets his mother's ex-lover go free and gets to complete his mission.
Ajay has a lot of missions for helping the locals by rescuing hostages or avenging their abuses by Pagan Min or even rescuing them from wild animal attacks.
Many of the Karma missions are designed around helping the locals, in fact.
The prayer wheel side-quest may seem to be strange until you realize Ajay is learning about his people's heritage and religion. Whether he believes in it or not, he finds it important enough to honor the locals' ways while fighting to free their land from tyranny.
Ajay's scenes with Bhadra. Though brief, Ajay is protective of her and cares enough to ask about well-being. With the Amita-as-Leader Ending, he even demanded to know what happened to her. And the player can make him shot Amita out of retaliation for Bhadra's implied murder. Bhadra in return, seems to like him, even hugging him with gratitude after Ajay rescued her from a burning building.
If you side with Amita and kill Sabal, her reaction seems is shocked and even a little bummed out. She apologises to Ajay that he did what was necessary. Also despite becoming just like Pagan (if not worse) post game, she did initially seem to care about the people of Kyrat in contrast to the more traditional Sabal.
Amita taking the time to personally teach Bhadra how to use a bow to defend herself. The other resistance fighters thought she was too holy to defend herself. You can tell Amita is one of the few people who sees a young girl in Bhadra rather than a goddess.
Amita also takes the time to help an old nun out with her wild animal problems. It becomes increasingly clear because of these acts Amita is more a Fallen Hero at the end rather than Evil All Along.
While Sabal acts courteous towards Ajay (assuming you take his side), he seems to see him more as an heir to his father's legacy than a person in his own right. Amita actually seems to care about Ajay himself, and confides in him about her past and her vision for Kyrat. When he escapes from Durgesh, the shot of her by his bed seems more tender than it does if Sabal is there.
A lot of Amita's reactions to Ajay's heroic deeds (rescuing hostages, transporting goods, etc) are kinder compared to Sabal. While Sabal eventually starts chiding the civilians about being in distress, Amita sounded glad and was happy that the people are free. This makes her downfall to becoming a drug-lord even worse.
Sabal's desperate The Men First attitude and his absolute devastation when he suffers losses.
During the Kyrati Fashion Week quest to go after the Sky Tiger, Chiffon radios in to tell Ajay to play it safe when tackling the legendary tiger. While he admits that his motivation for the caution is that you are his star (and only) model, there's a genuine concern that is a nice change from the typical aloof Mission Control you run into in these games.
Chiffon: I have been told that my clothes were to die for. Please don't prove that to be true. Stay safe out there, for both our sakes.