Unexpectedly, the pilot has one. Graham finds a lost dog wandering on the side of the road, then stops his car, turns the lights on, and opens the back hatch to let the dog in. When he takes the dog home, it's revealed that this is apparently a habit of his, and he cares for all his canine companions very well. Bonus points for showing a different side of Graham than his usual Good Is Not Nice.
Will Graham's relationship with Dr. Alana Bloom. She's genuinely concerned about him, and wants to protect him.
For that matter, his interactions with Beverly Katz. After a bit of a rocky start, she's clearly friendly and supportive of him.
Another moment with Alana — "I kissed Alana Bloom!"/"she's very kissable". Will's his usual brusque self and clearly kind of flustered after he blurts it out, but it's endearing.
After a rocky introduction to the Crawfords' marriage and the revelation that Bella has cancer and has not told Jack, the final scene of them coming clean to each other in Lecter's office is sweet. Jack's promise to be in her corner and be anything she needs is heartwarming, but what really seals it is when Bella finally takes his hand.
Despite the events that led to it, Hannibal's obvious relief when Will survives his run-in with Tobias is rather heartwarming.
Before that there is a temporary one in the same episode. When Hannibal is having dinner with Tobias Budge. He tells him that he's going to kill any law enforcement that investigates him and then he's going to kill Franklyn to which Hannibal replies "Don't kill Franklyn" it was a heartwarming moment until Hannibal snaps Franklyn's neck a few minutes later in the same episode.
Hannibal hugging a weeping Abigail, who has just confessed to him that her father forced her to recruit his victims. Hannibal assures her that she is a victim, not a monster and promises that he and Will are going to protect her.
Similarly, Hannibal's line "Office hours are for patients. My kitchen is always open to friends" sounds heartwarming to Will and terrifying to the audience.
In "Buffet Froid", Will finds Georgia hiding under his bed, and though he's clearly and understandably freaked out by it he gets down onto the floor, reaches out to her and assures her that she's alive.
Earlier in the episode, when he needs backup to support what he's found at the crime scene, he doesn't call Crawford, or the police — he calls Beverly. And, when he admits that he's not sure if what he saw even happened, all she says is "Then let's prove it," fully supporting and working with him.
Later, she is the one who checks him for bloodstains at a crime scene. She makes sure to tell him, "You're clean.", and insists to him that there's no way he could have committed the crime unconsciously; she's quite aware of his concerns and firmly reassures him without downplaying his worry. Beverly for best friend ever.
Jack Crawford tells Will that he considers him his responsibility. The whole time, we thought Jack didn't care how far he pushed Will, but it turns out, he does.
It was really sweet of Will to visit Georgia in the hospital and, in a bittersweet way, so is his concern about finding the truth about her death.
During the visit, he tells her that she's pretty and she gives him a beaming smile. D'awww.
Alana's relief at Will not being able to draw a clock properly, meaning he's suffering from a physiological illness and is not a deliberate serial killer.
Alana taking care of Will's dogs. Winston keeps going back to Will's house, like Hachiko.
Bedelia visiting Will in his cell and telling him that she truly believes him. Will looks overwhelmed with emotion. It's the small victories.
Crawford falling on his sword during his testimony at Will's trial, saying he's to blame for pushing Will past his sanity.
At the end of "Hassun", Will asks Alana what she wants, and she replies, tearfully, "To save you." Will moves his cuffed hands to hold hers, the one way he can express his gratitude.
From the beginning of "Takiawase", in Will's dream-river:
Will: Last thing before casting the line, name the bait on your hook after somebody you cherish.
Abigail: To say goodbye?
Will: If the person you named it after cherished you — as the superstition goes — you will catch the fish.
Freddie: Send someone else, Jack. She's one of yours.
In "Yakimono", we see Will's first truly happy smile since early Season 1, when he goes home and sees all his dogs running towards him.
Miriam receiving her prosthetic arm. She's almost in tears realizing that she has a left arm again.
Zeller, of all people, apologizing to Will, in "Su-zakana". Zeller, who gave Will the most grief in the first season, as well as being the most insistent of Will's guilt in this season, being openly remorseful and shaking his hand. There's just something really sweet and touching about the way he goes about it. And Will subsequently accepting it.
In "Su-zakana", Hannibal shows kindness to Margot by reminding her that she's not as weird as she thinks.
Hannibal: I'm much weirder than you will ever be, Margot. It's fine to be weird.
Will's compassionate treatment and fierce defense of Peter in "Su-zakana". Even though we're seeing the new Will Graham, who's taken a level in badass since getting out of prison and is attempting to go up against Hannibal in the Manipulative Bastard department, Will has not changed so much that he's forgotten what it was like to be falsely accused and unable to think clearly enough to fight back.
In the next episode, he goes to visit him while he's in treatment, and promises to keep quiet about the rat Peter smuggled in.
In "Shiizakana", the climax of the episode involves a shotgun-toting Will hauling ass to carry his wounded dog Buster back to the safety of his house.
As of the end of "Kō No Mono" it hasn't been made explicit, but we can surmise from Freddie being alive and in Jack's care that Jack believes and trusts Will. Perhaps more importantly, we can also surmise that Will reciprocates that trust, because the two of them seem to be working together to catch Hannibal. It also shows that Will isn't a murderer after all, his killings all being attributable to self-defense.
It seems that Hannibal actually does care about Margot on some level, as he makes sure to leave Mason alive so her family's money won't disappear, while still putting him in a position where he can never hurt her again.
Of a horribly sad variety, in "Mizumono": Will, lying on the floor and bleeding out next to the near-dead Abigail, uses his last strength to attempt to cover her wound. When he realizes it won't work, he holds her hand as they pass out together.
In a bizarre way, the reveal that Hannibal had planned to take Will and Abigail away with him, the latter of whom he specifically kept alive for Will's benefit and desire of a family/child. It all comes crashing down, of course, but that action shows that Hannibal genuinely cares for Will and wanted him to be happy with Abigail as a surrogate daughter.
Jack uses his final strength to call Bella while bleeding to death in Hannibal's pantry.