The prank war between Anakin and Ahsoka with Terriermon assisting both sides.
Terriermon's Running Gag of getting annoyed when someone uses his word, "momentai."
Once Palpatine learns that not all of his clones are following Order 66, he is practically twitching with anger. After he hangs up, this happens.
Palpatine stood up with a soul-piercing scream of livid fury and a burst of the Force shot out all around him, slamming cabinets and wardrobes and his chair into the walls all around him. His hands were curled like claws before him as he screeched at the ceiling in rage. How could this have happened? How could some clones have turned against him? They were hardwired to obey the highest authority – they were supposed to be no better than droids in that regard.
So why had some of them sided with the Jedi?
And, as great as it is to witness what is essentially a Sith temper tantrum, it gets better. Realizing that if some clones are siding with the Jedi instead of him, then more might be working against him. Thus, he contacts the clone who should have killed Aayla (who Palpatine had already failed to have assassinated twice by now and who would now know his identity as Darth Sideous).
His desk had survived his Force onslaught because it was attached to the floor, so he quickly called the communicator of a certain clone Commander at the other side of the Galaxy, eyes wide with apprehension.
Eventually, the clone answered, and Palpatine said, "Commander Bly, please report on your progress? Is Aayla Secura dead yet?"
The clone stared at him for a few moments, then pulled off his helmet and tucked it under his arm, smiling wryly at the Emperor. Then he said, "Why don't you ask her yourself?" His arm made a motion that indicated he was about to throw something and suddenly he vanished, indicating he had thrown the communicator.
A moment later, his hologram was replaced by the one person that Palpatine least wanted to see in the whole universe.
"You!" he growled. "You're behind this, aren't you? I just know it."
Aayla smirked at him. "You might say that," she said vaguely. "You've been trying very hard to kill me recently, Palpatine, but you're going to have to try a little harder. See you later. Oh, and by the way, congratulations on your new status as Emperor. Let's see how long you can hold onto it."
Suddenly, she cut off the communication, and several service droids many corridors away started in shock and almost malfunctioned at the incredibly loud howl of rage that followed.
Scorch, a clone with a particular talent for explosions, observes ZeedGarurumon opening fire and causing far more destruction than what he'd just done. The clone stared at the scene, stunned by the scale in comparison to his usual explosions, before exclaiming, "OH MAN! WHY MUST THE DIGIMON BE SO AWESOME?!"
At an important meeting to honor everyone who was involved in ending the war, in front of an audience that is composed of untold numbers of individuals and even some Senate members, Terriermon decides to act like... well, his normal goofy self.
Beelzemon's arrival into the Star Wars universe involved appearing... in the middle of traffic.
In Quest of the God:
Uxie, the Being of Knowledge, stating that the ultimate answer is 42
Uxie quickly improves Rika's opinion of him by simply making fun of Kazu.
Impmon, Ai, and Mako catching a glimpse of one of the Legendary pokemon they were supposed to be locating at the end of chapter 16, just as it vanishes across the ocean. How often in the games do you just accidentally find one of the wandering Legendary pokemon just for it to run away? Impmon's reaction matches those of hundreds of players when that happens.
The Royal Knights have a series of tests in place in order to only allow someone worthy to approach them. The instructions for these tests is written on signs. One of the signs for a particularly painful tests ends up reading LOL. JK. THIS WAS ACTUALLY ANOTHER TEST OF COURAGE. KAZU HAS FAILED THE TEST AND GUARDROMON IS DISQUALIFIED. THEY WILL BE TRANSPORTED BACK TO THE LIFT AT THE BEGINNING. THE REST MAY PROCEED. Who knew that Royal Knights use text talk?
In addition, during the first on-screen interactions with the Royal Knights, they get side-tracked from the conversation in order to discuss The Big Bang Theory.
Rika and Henry's reaction to Suicune's remarks concerning how the whole boyfriend/girlfriend concept is silly and that they should just go ahead and be mates.
The continued Running Gag of Terriermon's fear of pineapples reaches a hilarious level when he reacts similarly to an Exeggutor.
"So," mused the voice of the Son (who shall henceforth be referred to as Bogan even though he does not know he's been assigned the name) from nearby.
Once the Jedi realize that they couldn't wander around the Pokemon world wearing their normal outfits, they manage to get some other clothes. Obi-Wan ends up with a t-shirt that reads "'Who's the daddy?"
In To Be a King:
Sparrowmon's wake-up call after landing in Middle Earth consists of being poked with a stick.
In one of the first pieces of evidence that connects To Be a King to the other stories of the series:
"Nggh," a grunt from the slumbering Wisemon broke him out of his thoughts. "No. Don't come any closer. No… not… the pineapple! Anything but the pineapple."
"Oh, for Heaven Zone's sake," Beelzemon muttered. "Of all things to have a nightmare about… pineapples? Really? How can a pineapple possibly be scary?"
He bopped Wisemon on the head with the back of his hand again. "Huwhuh?" Wisemon blinked coherently. "Oh lord that was a bad one."
"About pineapples? Really?" Beelzemon muttered, deadpan. "Who in their right mind is scared of a pineapple?" he added, unaware that several dimensions away a bunny-like Digimon called a Terriermon sneezed at his words.