Leo and Mewgle's encounters, especially the first; Mewgle thinks Leo is either his arch-rival or soulmate when they first meet. It's the former.
Every single time Sam and Max are on screen something hilariously random and/or bizzare is bound to happen, such as invoking deus ex machine, weaponized Porn Without Plot, Rubber Pants Commandos, and game based fighting skills.
Anytime Leo's overwhelming nerd-ishness causes Pikachu to just spazz out. Later, Pikachu fanboys over the Pokerockers even worse than Leo.
Todd gathering up several warriors to fight Denchu and save Ash and the others...before telling them to go back out and redo the entrance, because he didn't get enough cool pictures.
The Running Gag of the Nihilator leaders (sans Oblivion's Shadow) being completely Ax-Crazy. i.e. Oblivion's Shadow mentions things like curing vampirism or health and safety, only for Bellum/Tarantulas/Chobin to stare blankly and make him go "right, forgot who I am talking to".
Nuken's reaction to being told that Missy's pregnant. Instead of going on a bloody rampage like you might think, he simply faints.
Anytime anyone says "what." anytime in the story. Leo causes many of these.
Pikachu's absolute horror when he realises his mother has just made an arranged marriage with Dawn and that nobody has a problem with it.
The Running Gag that Light of Justice is a Nice Guy that Richie would like to be friends with, if he wasn't crazy.
The fact that Richie's entire team and journey is an Expy of Ash's; their Big Bad is just a lot nicer. Which makes sense, Light of Justice is the reincarnation of N.
In Chapter 61, Ash begins to go into Void mode, just from hearing about Oblivion's Shadow. Briney simply smacks Ash over the head.
Dawn, Lily, Leo and Sasha watch chick flicks.
Every time the group goes off on a tangent which is Lampshaded many, many times.
In Chapter 63, Ash has a flashback where Mew tells him that even though he will suffer, everything will turn out alright if he relies on his friends and family. The flashback ends with Mew starting an orgy with Professor Oak, Riley, a Lucario and Delia.
This is followed by the horrified reactions of Ash's friends when he tells them what he'd seen.