Whistles & Sneezes, some boys throw stones at Henry. He gets his revenge on the return journey by "sneezing" all over them, covering them in ash.
Diesel 10's expression◊ when Mr. Conductor threatened to pour sugar in his tank in The Magic Railroad.
In Thomas' Trusty Friends, the construction team is sent to demolish a factory. They have to knock down a specific wall of the factory first. After an accident by Ned, the whole factory gets destructed in a marvoulous fashion. When we see the smoke clear, the wall they were meant to knock down first is still standing before slowly collapsing. The aftermath of the destruction for Thomas and Oliver the excavator is rather funny too.
"Just look what you've done to our breakfast!"
This is especially funny because before, Thomas had crashed into the stationmaster's kitchen and demolished a good part of his house's frame. The wife's response is to yell at him for ruining breakfast.
Another unintentionally funny part is of course the reaction when a similar accident happens of Duck crashing into a barber's shop. The barber is annoyed because he frightened the customers and decides to get back at the engine by covering half his face in shaving cream. The Barber and his customers are lucky to be alive, frankly.
The song some boys sing to insult Gordon in Off the Rails
Paxton interrupts a conversation that the Narrow Gauge engines are having to tell them he's covered in rubble and he needs help at the beginning of Blue Mountain Mystery.
Bill and Ben's arguments from Season 17. Their new accents help too.
In "Thomas, Percy, and the Dragon", Percy, who has to stay in a siding until the jammed points were repaired, has a speechless reaction after his crew tells him that they are going home for tea.
Whenever Sir Robert Norramby is on scene.
Especially his first scene. To give you a summary: Everybody throws Sir Robert a party at Knapford Station. When he arrives on Spencer, everybody cheers and the Brass Band plays. Robert, gets out of the coach, just waves at the people, says "Oh, who's the party for? Anyway, I must go" and gets in the coach again. The band plays while they leave the station and everybody is shocked.
In the ending of "The Thomas Way", Duck discussed with Thomas that there are three ways of doing things - The Great Western Way, the wrong way, and The Thomas Way, yet The Great Western Way is usually the best. Cue to both engines laughing.