* [[RunningGag Pikachu once again blows up Misty's bike.]]
* Prof. Oak choking after Ash tells him about Celebi.
* Ash wondering if a Surkit (Bug/Water Pokemon) will cause Misty to short circuit.
* Ash telling Misty to teach her Staryu Power Gem or get a Fire-Type.
* Blind luck dropping a knocked-out Pidgeotto right next to the gang (Ash and Misty at the time).
* Pikachu remarking, "Brock isn't an idiot unless women are involved."
* [[ShamuFu Misty's slapping Brock with her Goldeen.]]
* A mad Pidgeot telling Sir Aaron's Lucario that it's a female.
* Ash brings the Cerulean gym's roof down.
* James's Wheezing laughing at Jessie's Arbok after getting Abra and Cubone on the team.
* Damion losing his control.
* James looking for a Gym to fight in using a guide made by "Prima". In the real world, "Prima," is a company known for making game guides.
** Doubles as MythologyGag: in the actual anime, the Elite Four member Lorelei got a DubNameChange into Prima, and, when Team Rocket taunted her by asking if her lectures were on CD [[CrowningMomentOfFunny she replied they were on tape only and costed 18.95 Pokemon Dollars]], causing general FaceFault that included even the ''Team Rocket balloon''.
* The ninja Meowth remarking to Team Rocket's Meowth, ""They're taking the gym challenge, I know where they're going. You don't think we have to run an obstacle course every time we need a pint of milk, do you?"
* Bulbsaur overdoing the Growth job and accidentally evolving into a Ivysaur.
* Ash remarking ""Not only no, but HELL no" about Maiden's Peak.
* Palkia, the Titan of Space, smiting Sir Aaron's character sheet because of a bad break-up with Kyogre.
** Not only does the character sheet get smited, but it gets compressed into ''neutronium.''
* The Indigo League commentator remarks after Ivysaur takes down a Jaxon's Muk: "Okay, ladies and gentlemen, after a talk with our local Joy, I can tell you that Jaxon's Muk is not permanently harmed. If you have a piece of sludge near you, those in the front rows, please signal and a bag will be provided. Muk is going to be reincorporated later, and will be fine so long as not too much mass is missing."
* Ash and the company talking about the Australian Dragonite King.
* Growlie (now an Arcanine) and Brock's Ninetails, performing a ShoutOut to LadyAndTheTramp.
* Anytime the story cuts back to Arceus, Aaron, Palkia and Dialga. Mostly because Palkia and Dialga keep cheating anytime they play a game.
* The fact that Squirtle, who was fairly normal in the original show, is now a fan of TengenToppaGurrenLagann. He even has his own equivalent of the Giga Drill Break.
** And now he's apparently got Gary's Squirtle in on it, complete with Simon's Star-Shades. Also, he had his own pre-time skip Simon equivalent back in the Squirtle Squad.
** It turns out that ''all'' of Squirtle's evolutionary line are massive {{Otaku}}. Case in point? The island of Squirtle Evolutions are now [[Manga/{{Naruto}} The Hidden Turtle Village.]]
** The Wartortle Firefighting Squad of Ascorbia Island are the [[Franchise/{{Power Rangers}} Wartortle Rangers]]
* [[RunningGag If Squirtle, Pikachu or Riolu are involved in a gym battle, there's a good chance that the gym will be destroyed.]]
-->'''Ritchie''': Yeah! Actually, now I think about it I do recognize you. You're that trainer they were calling the Gym Destroyer on the TV commentary, right?
-->'''Ash''': I didn't know they were calling me that. Though I have to admit it's pretty accurate...
* Ash stating that, using Aura Purge, he'll get rid of Misty's fear of Bug types. Riolu says that Misty'd kill him if he suggested she's weak. [[TooDumbToLive Ash]] says he'll use "Tact and Diplomacy". Riolu simply sighs and replies with "You're Doomed."
** Followed up by Ash threatening Misty that either she takes the painless Aura Purge to get rid of her fear of Bugs, or Squirtle "Fixes" her with sheer distilled awesome, possibly involving tearing open dimensions, rock music from nowhere and punches.
*** Even funnier? Squirtle ''still'' manages to at least partially fix her using Gurren Lagann logic.
* Dexter, Dee and Damos have their own little nickname: [[spoiler: The Three Pings.]]
* Pikachu and Riolu. If they're not arguing, they're snarking about something.
* The one second long "Fight", if you could call it that, between Pikachu and Surge's Raichu.
* This exchange between Jessie and Butch.
-->'''Jessie:''' "Well, well, wouldn't have expected to meet you here, bit-"
-->'''Butch:''' "[[ComicallyMissingThePoint It's]] [[MythologyGag BUTCH]]! [[AccidentalMisnaming Why can nobody]] [[RunningGag EVER]] [[AccidentalMisnaming get that right?]]"
* The punks tormenting Lapras. [[WhatAnIdiot They're so stupid that]] ''[[IdiotHero Ash]]'' was the OnlySaneMan in that scene.
-->'''Ash:''' "I just... I've never heard so much stupid in one place."
* Misty said that Ash can be a little obsessed at time. Ash's reply? An angry "[[IResembleThatRemark I resemble that!]]". Promptly [[LampshadeHanging lampshade]] by Lapras and Pikachu.
* 'Prima''s lecture is funny beyond explanation.
* Ash's reaction to Misty declaring "[[TemptingFate Well, all's well what ends well]]": [[GenreSavvy diving for cover]]. It took him a while to accept there was no [[MythologyGag Legedary Pokemon showing up from nowhere, random airships crashing down, or anything else]].
* In this fanfiction, a SWAT team is composed by [[FunWithAcronyms Sandslash, Wartortle, Alakazam and Tangela]]. [[LampshadeHanging It USED to stand for something else]], but someone missed got confused somewhere...
** Special Weapons and Tactics, out 'here.'
* Ash on Crossdressing "It was bad enough the first time, worse the second time, and not quite as bad the third time, which is what really worries me" Cue Kricketune!
* Lugia showing up in chapter 41 to stop the Legendary Birds:
-->''I have no idea why you three'' keep ''doing this. What was it this time?''
* When you consider how many hilarious antics occur in the story, the very fact that we are attempting to count them all is a Meta-example.