Albert's speech about being an adamant pacifist, particularly at the end when he says "I love you, Sheriff Truman."
The scenes where Ben Horne looks back on his childhood are both heartwarming and funny.
The night Catherine comes back home to Pete in her Tajemura disguise. The look on his face when he realizes it's her made this troper crack a smile from ear to ear.
In Fire Walk With Me the final scene where a despondent Laura, trapped in the Black Lodge, is visited by the angel that she thought had abandoned her. Her sudden realisation that she was still a good person worthy of love and protection, despite the terrible experiences she had suffered, was a truly heartwarming moment.
Agent Cooper appearing along side Laura in the Black Lodge, comforting her after all that she's been through. It goes to show that despite being possibly trapped there for what may be an eternity, his optimism and compassion haven't waned. He fulfills his mission as the detective in Laura's case beyond simply solving her murder, but putting her to rest as well.
Major Briggs telling Bobby about his vision of Bobby's future happiness. By the end of his speech Bobby is literally in tears.
Maddy Ferguson's final conversation with James where she tells him that he and Donna belong together, and that essentially being Laura in many people's eyes was fun for a while but she has to return to reality. This is subject to severeMood Whiplash come the next episode.
Cooper guiding Leland into heaven, and then telling Sarah how peaceful his death was.
Cooper's would-be exit from the town, with Harry giving him a fly lure and a Bookhouse Boys badge, and his perfect sendoffs to Hawk, Andy, and Lucy.
Despite Audrey being an eighteen-year-old girl with a big crush on Cooper (and admittedly quite sexy), Coop never treats her with anything but the utmost respect and kindness. When she attempts to seduce him in his hotel room, he gently turns her down, and offers to just be her friend instead, sensing that a friend is what she really needs right now, and leaves to get some ice cream for them to share before they have a talk about Audrey's troubles. The scene is easily the most heartwarming in the series.
Many of the scenes between James and Donna can be this, especially when the latter comes to realize how much she loves him.
The picnic scene after the whole Evelyn matter stands out as Donna forgives James for running out on her, and tells him to get away from it all so he can have memories which aren't related so the horrible events in Twin Peaks, even saying that she'll miss him and be waiting for him the whole time.
Cooper in general is a heartwarmingly good and loveable character. The same can be said for Garland Briggs.
His entire relationship with Truman is particularly sweet. They hit-it-off almost immediately and spend almost the entire series helping each other. Truman never objects to Cooper's strange requests and Cooper quickly demonstrates his appreciation by siding with him in Truman's initial conflict with Albert.
Bobby turned his life around and joined the police force. He now specifically looks to rid Twin Peaks of the same waste of space drug dealers he was in 1989.
During the Time Skip between seasons 2 and 3, Denise was promoted to chief of staff of the FBI. Cole's revealed to have supported her the whole way.
Cole: Before you were Denise, when you were Dennis and I was your boss, when I had you working undercover at the DEA, you were a confused and wild thing sometimes. I had enough dirt on you to fill the Grand Canyon, and I never used a spoonful because you were and are a great agent. When you became Denise, I told all of your colleagues, those clown comics, to fix their hearts or die.
The moments when Cooper, in his addled Dougie-state, starts to seem most like his old self and act independently are when he's able to help other people or make some kind of empathetic connection with them, like guiding the old woman in the casino to a winning slot machine, offering Sonny-Jim a potato chip, or protecting Janey-E from Ike.
The old woman from the casino returns in part 11, thanking Cooper for changing her life and reuniting her with her son.
In part 15, Ed and Norma rekindle their relationship after Ed receives Nadine's blessing.
While Cooper's awakening by itself is this and a Crowning Moment of Awesome, he shows that he hasn't lost his kind personality over the years he spent in the Black Lodge, or in his amnesiac Empty Shell state. When the Mitchum brothers show concern over his true identity, he simply tells them that they have "hearts of gold" and as such, nothing to fear. And his first instinct upon awakening is to ask MIKE to create another Dougie for Janey-E and Sonny Jim.
MIKE creates another Dougie. Janey-E and Sonny Jim are elated to see him again.
Many actual survivors of incest came forward over the years to thank Sheryl Lee for her portrayal of Laura and what she goes through in Fire Walk With Me.
In 1992, when Fire Walk With Me played at Cannes, it was greeted with a negative response and much booing. 25 years later, the premiere of the third season was received with rapturous applause, and there was much cheering for David Lynch in particular.