In "Edward, Gordon, and Henry", Gordon breaks down in front of the tunnel where Henry is walled up. Since Gordon has been taunting Henry about his predicament for months, Henry -and the audience- both enjoy a good laugh at Gordon's expense.
Thomas In Trouble: Thomas telling the Policeman that he doesn't catch cows when the policeman asks where his Cowcatcher is.
From the same episode, yelling "Oi, You!" at Toby, when Toby rings his bell at him and frightens him.
Thomas and Edward's exchange at the start of "Saved from Scrap"
Edward: I'm going to the scrapyard today.
Thomas: What, already? You're not that old!
This Exchange from "Tender Engines":
Duck: I wouldn't drink all that water if I were you. It might give you boiler ache.
Gordon: Pah! What's this? Educating Gordon day? First James, now you, Duck! Big Engines have big needs, little engines are just annoying.
Duck: Don't say I didn't warn you.
Toby and the Stout Gentleman: Bridget mistaking Toby for an electric tram is good for a laugh.
Off The Rails is particularly amusing, as Gordon is being more pompous than usual, thinking how large and splendid he is. Henry arrives and completely destroys that image by calling "Peep! Peep! Peep! Hello! Fat face!".
Most of Lady Hatt's Birthday Party. The Fat Controller's attempts to get the party. The whole journey was downright hillarious.
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.
Lady! He nearly crushed you and your family! Get some perspective!
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.
In "Splish, Splash, Splosh!", Thomas splashes through a puddle, sending water on top of the Fat Controller and Alicia Botti. As it comes down on them, the Fat Controller tries, in vain, to shield Alicia with his top hat.
Percy falling into a pit of moat alongside Stephen in "The Phantom Express". Then Stephen says, casually, "I see you've found the meeting place."
In "Not So Slow Coaches", Annie and Clarabel are accidentally coupled to Caitlin's train, causing them to panic when Caitlin accelerates down the Main Line.
Annie: I don't like this at all!
Clarabel: I've got my eyes closed!
Annie: Does it help?
Clarabel: No! Not really!
In "Disappearing Diesels", the diesels are hiding from Paxton as part of a joke. Den and Dart are hiding behind a line of trucks. Paxton calls out if anyone's there. Den says "No" out loud... and then Paxton rolls away.
Diesel breaks down and becomes stranded on the line while trying to hide from Paxton, who catches up with him. Diesel explains that he was trying to hide from Paxton as part of the prank he's been playing on him all day. His response? "Well that's not a very good hiding place."
In "No Snow for Thomas", Thomas' reaction when he sees Emily pulling Annie and Clarabel. Emily then promptly rubs it in his face.
"The Smelly Kipper" has a great deal of humor around the engines' playful teasing of each other. First we have a cocky James agreeing to Henry's dare to pull the Flying Kipper. After he eventually changes his mind, he manages to slyly convince a groggy Henry he just dreamed the whole thing. However when the Fat Controller comes to query the whole thing, Thomas and Gordon point out James really did agree to Henry's bargain (complete with hilarious "busted" smirks). The following morning James comes back, irritable and smelling of fish ("I...had a little accident!"), the other engines erupt in laughter.
Gordon:*laughing, eyeing the fish on his buffer beam* Look, he's brought a present for the Fat Controller.
Bill and Ben tricking Connor (twice!) in "Bill or Ben?". And the scene where Ben tricks Kevin into repainting him while Victor is away.
The part where Percy kept annoying Gordon and James at the start of "Duck Takes Charge". This exchange in particular:
Percy: Do you know what? Gordon: What? Percy: Do you know what? Gordon: Silly! Of course I don't know what! If you don't tell me what 'what' is!