Hicks using his power to help Gary in "Anger Management", causing Gary to look genuinely happy for a brief moment, which nothing up to that point had done.
Bill telling Gary he's a 'good partner' in "Bill and Gary's Excellent Adventure".
Dr. Rosen's speech to Rachel about how special she is to him in "Never Let Me Go."
Bill fulfilling his promise (that he had earlier reneged upon) to let Gary drive in "Bill and Gary's Excellent Adventure."
Skylar's happiness at the end of her episode ("Catch and Release"), and the little ditty that her daughter makes for a formula.
Gary encouraging Rachel to tell her father to see a doctor, and the resulting conversations between Rachel and her dad in "A Short Time In Paradise."
Rosen's whole attitude towards Alphas, and his team in particular. Like in "Cause and Effect," when he tells Agent Sullivan: "It's not us vs. them. It's us and them. That's the only option."
Or in "Rosetta," when Gary has been upset throughout the episode.
Rosen: Gary, I know you liked Anna, but I'm your friend too. Gary: Yeah, I know, but—you're not one of us. You're not. Rosen: ...Gary, I don't make distinctions like that.
In "Wake-Up Call", when a traumatized Gary is refusing to speak, and the entire team tries to talk to him (Rachel gives him hummus, Bill reminds him of his schedule) before Rosen finally gets him to call his mom and he starts talking. Rachel, Bill, and Nina all hug him in quick succession, despite his objections.
In "The Quick and the Dead," Stanton Parish and his dying granddaughter. He brings in Dani to help soothe her pain. It turns horrific at the end of the episode, however.
Dani's willing to stand up to Stanton Parish himself in order to continue seeing Cameron. And he's so impressed by her candor that he lets it happen.
In "When Push Comes To Shove", after everything Nina's gone through (and done), she's hospitalized/arrested and blindfolded to prevent her from using her power to escape. Rosen walks in, calmly removes the blindfold despite Nina herself protesting, and greets her like they're two old friends. It's scenes like this that show why Rosen can keep the team together.
One from Agent Clay in that episode: He got Nina released into Rosen's custody with no criminal charges. Especially heartwarming when you realize that he probably had to really stick his neck out with his bosses to make that happen.
A big one from Hicks: Nina tells him "You're free; do whatever you want" and what he wants is to save her from committing suicide. Even after everything she's done, he cares enough about her to want her to live.
Gary's subplot in "Alphaville". He starts off upset because the town is one bigdead zone. Then he discovers how much fun stargazing can be when you're a living radio telescope. By the next day, he's decided he wants to live there. Which makes the ending even more of a Tear Jerker.
In "Gods & Monsters", Rosen responding to Parrish's earlier threats against Danielle by confining him to a prison cell once he doesn't need his help anymore, capping it off by telling him "You shouldn't have threatened Danielle." Even though Parrish escapes, this nicely demonstrates that you mess with Rosen's loved ones at your own risk. Doubles as a Crowning Moment Of Awesome.
In a darker way, there's Parish leaving the Alpha Utopia he intends to create for Rosen, believing there's No Place For Him There. It is a rare moment where Parish actually seems emotionally vulnerable. Keep in mind this guy intends to comitt mass genocide on our planet, yet he leaves his utopia for a common human
"Oh, yeah, Mom? I'm glad you're not dead." That's about as publicly affectionate as Gary gets.