Delibird using Fly. Seeing a penguin flying whilst carrying a person three times its size would be funny enough, but the first time we see it happen, the Delibird refuses to let go of the bag on its back, meaning that it achieves flight by furiously flapping a single arm. It's hilarious.
Diamond and Pearl's manzai scenes. They're funny indeed.
Mars' first appearance in the DP arc, where she ends up answering the punchline to Dia and Pearl's comedy routine when Dia actually forgets it.
Platinum dances. The next panel shows Dia cheerfully copying her, while Pearl has a WTH? look on his face.
Dia and Pearl's comedy routine to Fantina results in Fantina laughing at it even though she has a vague understanding on what it actually meant. She laughs when repeating the joke herself, too!
Dia's one-shot gag. What's funnier is that no one else except Fantina seems to find it amusing.
Crasher Wake putting Pearl's heading through the Croagunk Wall, you then see then see a picture of a Croagunk with Pearl's face on it! Even his Pokemon were laughing at this!
When the Sinnoh gym leaders fight Team Galactic at Mt. Coronet, Byron provides underground support... like digging a hole underneath Gardenia's Cherubi before Mars' Purugly can KO it. He gives Cherubi a quick healing, then it pops back out of the ground and kicks Purugly in the face with its stubby little legs.
White seemingly losing her cool at Black for letting Tep evolve, only to reveal that she was just kidding.
White's first try at catching Deerling, then running around in circles trying to escape from it. Black's sweat drops, considering his regular Large Ham attitude, are quite funny to look at.
Iris visits Burgh in Castelia City while he's showing off a new creation, and he asks for her honest opinion. She does... with Brutal Honesty. Cue Burgh acting devastated, complete with Iris's word balloon spearing him through the heart.
Black vs. the Black Empoleon biker gang. First, Black trashes their bikes, leading them to exclaim things like how they hadn't finished paying the down payment or how the bikes were a gift from their mothers. When only the leader is left, he discovers that Black's Musha used Teleport to transport the bike's expensive premium fuel straight into his pants.
The author notes, especially the recent ones. The artist usually starts off by making insightful comments about the current themes or characters. This will be followed by the author completely fanboying about the games or going on about some random facet of his life, like how he bought a car on impulse just because the color it was painted in was called "Royal Ruby Red Pearl."