In Bidoof's Wish, Wigglytuff tells the guild that it's Bidoof's exploration, and thus he should be the only one to meet Jirachi (and have his wish granted). After Bidoof leaves, the guild then notes that Wigglytuff is quite generous for giving this chance to Bidoof, given that he could've wished for all the Perfect Apples he can eat, then starts cheering about how generous he is. Then...
Wigglytuff: I'm going.
The guild having to physically restrain Wigglytuff to prevent him from doing so.
Wigglytuff: I have to go with Chatot? That's so booooring!
Wigglytuff claimed that he lost the Unown key, but when Lopunny gave him a Perfect Apple, he YOOMTAH'd and made a mess of his room and found the key.
Wigglytuff "befriending" Uxie and a Groudon illusion.
The scenes where Team Skull tried to assault Wigglytuff.
Sometimes Pokémon you've befriended show up, including Legendary Pokémon, and they run away from the explosion freaking out.
One from "Igglybuff the Prodigy":
(Armaldo is musing over the wonders of exploration with the melancholic "Beyond the Dream" playing in the background; the music suddenly changes to the upbeat "Guildmaster Wigglytuff" when he spots Igglybuff burning a valuable map)
Igglybuff: Ha ha ha! ♪ Burned it, burned it! ♪
Armaldo: H-hey! Junior! What are you doing?! Knock it off! (he snatches the map - burning himself in the process - and panics (Hot hot hot hot HOT!!!), searching for water, only realizing a few seconds later that he can use Water Gun)
Pfft, what about when Igglybuff and Armaldo find a room with a door controlled and guarded by myriad traps, many of which seemingly lethal, that Igglybuff just disregards and BREAKS THE DOOR OPEN?
Made even better by Armaldo's reaction
Armaldo: What in the world IS this kid!?
From the first Special Episode, Bidoof is given a wish from Jirachi, with several choices appearing. No matter what you choose, Bidoof thinks about it before choosing his original wish. What's one of the choices? To Take Over the World! Made even better by Bidoofactually considering it if you choose it.
The list implies these were all the first wishes Bidoof could think of off the top of his head. That says something about Bidoof.
Try scoring a 0 in the Sentry Duty minigame. Both Chatot's and Loudred's reactions are hilarious.
One from the Explorers Of Time And Darkness anime. After Chimchar and Piplup get registered, Wigglytuff starts talking. We get shots of all of the guild members getting really scared looks on their faces, and we see why when this happens:
Wigglytuff: Registered? All registered! Yoom-TAAAAAAAAAAAAAAH! (Hyper Voice blows everyone away)
The Reviser Seed. It revives your Pokémon like a Reviver Seed, but then it notices that it's an "s" instead of a "v", and your Pokémon bursts into spontaneous laughter and faints. So, yeah. They basically kill themselves laughing.
The Itemizer Orb turns a foe into a random item. Seemshorrifyingat first, but it can be hilarious. That pesky Nidoqueen isn't so high and mighty when you're wearing her as X-Ray Specs, selling her to Kecleon, or making her into a beverage at Spinda's bar.
The "selling her to Kecleon" sounded so wrong, even though Nidoqueen can't breed...
When Wigglytuff Leaves the guild for a bit to talk to Lapras Chatot announces that he will be in charge in Wigglytuff's absence. Cue silence from the rest of the guild.
Special mention goes to Bidoof for being an in-universe example of Nightmare Retardant by screwing up the whole fighting-in-the-dark thing. Also, to Loudred for freaking out at remembering his graduation attempt, only to be one of the "minions".
After you and Grovyle return from the future, the scene when Chatot pretends to not know your story is hilarious:
Chatot: Ahem! Let me summarize your story so far... First... Grovyle is actually a good Pokémon...? And he was collecting the Time Gears to save the world? (partner): Yep! Chatot: And the great Dusknoir only pretended to be kind and helpful...? But he was actually a heinous and wicked villain? (partner): Yep...though I didn't really phrase it as "heinous and wicked"... Chatot: Also...(name) is really Grovyle's partner? (partner): Yep. Chatot: So Dusknoir wanted to get rid of both (name) and Grovyle...? So he took them to the future? (partner): Yep. And me too. Chatot: Then you managed to escape from Dusknoir by the skin of your teeth...? And you barely made it back home from the future? (partner): Yep. Chatot: And finally, this planet will soon become paralyzed...and to prevent that... Grovyle has started gathering Time Gears again? Meanwhile, you two are looking for a place called the Hidden Land? Is that your story in its full entirety?! (partner): Yep! That's all of it! Chatot: (Beat) Hee! Hee-heeee! Hee-heeee! (partner) and (name)... You must have had a bad dream or something! (partner) (questioned): What? And so on.
It's almost a shame that most skilled players won't faint in dungeons very often, because some of the game's finest moments of comedy come through its see-through attempts at justifying why you would ever fall for the exact same traps and fight the exact same boss battles when you clearly knew it was there and how to avoid it. Some highlights of these moments include Armaldo and Igglybuff managing to fall into a pit they already knew existed ("Wow, Master, you must really like pits!") and Wigglytuff having to forcefully shove the player into a pit because that's the only way he could possibly get you to finish your graduation properly when you already knew it was coming.
Loudred pretending to voice the sea and roar at Dugtrio to get back to work. It was Diglett who came up with it.
The wake-up call you and your partner get from Loudred each and every day at the Guild.