In "Edward and Gordon", there's Gordon ranting angrily when he is pulling a goods train instead of the express, much to Edward's amusement:
Gordon: "A goods train! A goods train! A goods train! A goods train! The shame of it! The shame of it! Oh, the shame of it!"
Later, as Edward came to push Gordon's train up the hill, he tells Gordon that's he ready. Gordon grumpily responds "No good!"
In "The Sad Story of Henry", The Fat Controller tells the passengers that his doctor had forbidden him to pull and push the Henry out of the tunnel.
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.
Also, there's The Fat Controller leaning out of the window to wave at Edward and Henry, but the train was too fast that his top hat blew into the fields that a goat came to eat it, much to The Fat Controller's dismay.
In "Thomas and the Breakdown Train", there's Thomas' expression as he watches James being lifted by the breakdown cranes.
In "The Flying Kipper", there's the dialogue between the driver, fireman, and conductor inside the brakevan.
Conductor: The Kipper is due. Fireman: Who cares?! This is good cocoa.
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.
Toby and the Stout Gentleman: Bridget mistaking Toby for an electric tram is good for a laugh.
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.
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!".
The song some boys sing to insult Gordon.
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!
The part where Percy kept annoying Gordon and James at the start of "Duck Takes Charge" in this exchange:
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!
In "Percy Takes the Plunge", there's the scene where Thomas reminds Percy of the time went past danger and fell down a mine. Percy, confused, states that he can't see a mine.
Another unintentionally funny part is of course the reaction when a similar accident happens of Duck crashing into a barber's shop in "A Close Shave". 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.
Stationmaster's wife: "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!
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.
From "The Trouble with Mud", there's one moment when Gordon bumps the trucks one by one.
Gordon: That's for you! And you! And you!
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.
From "Percy, James, and the Fruitful Day", Percy gets covered in fruit after an accident. The Fat Controller gives him this lecture:
The Fat Controller: "Percy, you are not to blame for the switch failure, but I do not run a jam factory!"
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 marvelous 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.
Gordon's reaction when Percy informs him that he's temporarily in charge for today in "The Green Controller".
Bill and Ben's arguments from Season 17. Their new accents help too.
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.
During the seasons animated by Arc, you can't help but feel Thomas' face is a constant Crowning Moment of Funny, what with all the eye rolls and mischievous looks he gives.
James supplies well in this area as well, Arc does great conveying what a smarmy bastard he is.
The ending to "Old Reliable Edward" has quite possibly the cleverest usage of Gordon's infamous catchphrase of all time.
Edward: And what do you say? Gordon: Oh, the indignity... Edward: Sorry? (smug look) Gordon: I mean...thank you. Thank you, Edward.
Henrietta's face when James and The Fat Controller find out Toby was right about the signal in "Signals Crossed."
Plus, forcing James to apologise to her as well as Toby (albeit as dryly as possible). Also a MOA.
In "Duck in the Water", we're briefly treated to a scene with some ducks swimming across the flooded track right in front of Duck, who is waiting to be pulled out. Duck's face tells you everything.
Also, Duck's rather annoyed "Can I get out of the water now?"
When the Fat Controller first enlists James (who was pretty much begging he wasn't going to pick him), the engine makes every possible excuse not to fetch Duck, even getting snarky with his boss. Made even funnier due to the Fat Controller's deadpan treatment, as if he's had this argument with James a million times before.
"Duck and the Slip Coaches": Emily pulls up to the sheds and sees that all the births are full because Duck is staying the night. Disheartened, she sighs and goes away. Then, at the end of the episode, she finds a spare birth...only for Henry to speed past her and take it.
In Marion and the Pipe, Marion's face when she tries dumping dirt on the leaking pipe.
The way she clears the boulder off Gordon's line. "FORE!" *thwack*
This is probably more worthy of a facepalm, but in "Missing Gator", Percy gives us the absolute most brainless rhyme in all of the show. (It sort of Makes Sense In Context though.)
Percy: Keeping busy, keeping busy, never thinking isn't easy! Push some more trucks down the line—who needs thinking? I feel fine!
Ben's "nyah nyah!" to Timothy in "No Steam Without Coal". His facial expression is priceless.
"Spencer's VIP" has the annoyed Deputy Minister giving the Fat Controller a newspaper while voicing how unreliable he thinks Spencer is. Just look at what the Fat Controller's doing there—he actually thinks it's his award for a few seconds.
And then there's Oliver shutting up Duck in the middle of his "Great Western Way" spiel.
"Toad's Bright Idea" has Oliver catching himself short on a bad pun.
Oliver: See you later, Gator! In a while, um...Toad.
"Misty Island Rescue" is goddamn funny if you take the time to lampshade the rhyming and the Fridge Brilliance-s.
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.
The resolution of the "Special Coal" issue in King of the Railway.
Toby: Henry's broken down! Gordon: Don't tell me he needs Special Coal again... Toby: No, Gordon, that was fixed years ago!
Quite a few from Tale of the Brave. Seriously, it flips between Awesome, Heartwarming, Tear Jerker, and Funny incredibly rapidly.
Marion being a Motor Mouth is quite funny, especially when she says "And chickens!" when talking about big animals.
Armageddon erupts in the docks as Porter rushes in shouting about Runaway Trucks, Percy rushes in shouting about a monster, Cranky panics and drops a bunch of sandbags on Thomas, and even Salty looks visibly worried...then Gator just rolls in and says "Oh! Hello!" like it's any other day.
Gets even funnier when Cranky denies thinking he was a monster, only for Thomas to clear his throat and give him a look.
The quick jab at Season 15's Up, Up, and Away!, especially because Thomas pulled that response out of nowhere.
A horrified Thomas, Annie and Clarabel thinking that James is getting scrapped, when really he's just going to collect scrap.
Emily's Ironic Echo of a teasing remark James made towards Percy, as James is forced to pull the Flying Kipper that night.
James goes into a panic and derails while pulling the Flying Kipper...just from Gator greeting him.
Right after the red engine runs away, Gator groans that he scared another engine away, as his driver walks over and turns his lamp on much too late.
Thomas tricking an apathetic James into helping him just by asking if he's scared. James immediately opens his eyes. Cue Gilligan Cut of James storming off to find Percy with a very smug looking Thomas following.
Sir Topham Hatt of all people using one of the engines' catchphrases when he finds Percy disappeared during the presentation of the fossil.