There's the moment where Henry is let out of the tunnel after The Fat Controller asks him to pull the heavy express.
In the ending, Edward and Henry take Gordon back to the sheds, thus cementing the three's friendship.
James the Red Engine
In "Troublesome Trucks", there's James sincerely apologizing to the Fat Controller for causing trouble with the coaches, prompting the Fat Controller to forgive him and let him out of the sheds to pull some trucks. It gets better in the end of the episode where the Fat Controller reveals himself after James finishes the arduous job. James is worried he's in trouble again, but the Fat Controller smiles and commends James for dealing with the trucks and allows him to keep his red paint, signaling that James has already on good terms with him.
In "James And The Express", after Gordon suffers a mishap, James is left to pull the Express in his place. Rather than the usual formula with the pompous engine humiliated and upset, Gordon is revealed to be impressed with James' work and encourages him to keep up the good work. The narration explains that James pulls the Express to give Gordon a rest every once in a while and the two cement their Vitriolic Best Buds relationship.
Henry the Green Engine
In "The Flying Kipper", Henry returns from crewe and is greeted with a warm welcome back from the people at the station and is cheered for his new shape.
Gordon the Big Engine
In "Down The Mine", Thomas and Gordon "formed an alliance" after learning how they are in disgrace for their misbehavior (Gordon falling into the ditch and Thomas falling down the mine).
In "Paint Pots and Queens", the two vouch for each other to the Fat Controller with Gordon asking if Thomas can run his branch line again while Thomas requests that Gordon can pull coaches again.
Duck and the Diesel Engine
In "A Close Shave", after Duck stopped 20 runaway trucks from hurting passengers by crashing into a barber shop, the barber yells at him without knowing the scenario. When the Fat Controller explains what happened, the barber is immediately sympathetic.
Barber: I'm sorry. I didn't know you were being a brave engine. Duck: That's alright, sir. I didn't know that either.
Along with Duck being told that he can come home, he rolls into the shed, greeted by whistles of all the other engines.
The Twin Engines
A small one, but it's comforting to know that after the last potential newcomer on trial, Duck actually hits it off right away with the twins.
How all the engines jump to Donald and Douglas' defence in the last story, despite their accidents. The two aren't officially part of the railway yet, but it still sends a warm feeling into your heart. And the ending where everyone's whistling for joy, is a grand payoff.
Main Line Engines
In "Buzz, Buzz", Duck's dislike for diesels was remedied after BoCo came to the sheds and revealed that he was a friend of Edward.
Edward, who's often mocked for being the oldest engine, uses everything in him to pull a train after a serious breakdown. He shows up late at the station, but the passengers are so proud of him that they give him a round of applause.
There's also Donald and Douglas being the last of the engines to accept BoCo into the family.
Douglas didn't hesitate for a moment after hearing Oliver's story about being in the scarpyards, and sets about to smuggle them to Sodor. Made more heartwarming when you realise Douglas is following in his older twin's footsteps.
Oliver The Western Engine
Donald instantly taking to little Dilly, even after discovering it was a prank by Duck. In the TV show, Donald even calls Dilly his 'Quackerroo'.
Duke The Lost Engine
Granpuff is this, and a Tearjerker rolled into one. The bond between Falcon, Stuart and Duke is beautiful, a mix of the mentor/student and father/son relationship. Which makes their separation super depressing, and they were like this for twenty-two years!
Sleeping Beauty is a fantastic payoff for the whole SkR arc. Duke is found and sent to the SkR and reunited with Sir Handel and Peter Sam, and their bond hasn't changed at all.
James and the Diesel Engines
In "Deep Freeze", James becomes more accepting of diesels after one of them had helped him after his injector fails.
More About Thomas the Tank Engine
In the ending of "Drip Tank", there's Thomas apologizing to Percy for his behavior towards him throughout the start of the book, especially when calling him a drip. Even more heartwarming when he asks that both of them can be friends again, which makes Percy happy.