At the start of the second chapter of the game, you are stalked by your partner, and then, when your partner introduces themselves to you, they proceed to push you to town. Then this happens:
Partner: ...Hmm? Am I annoying? You're totally thinking about how annoying I am right now, yeah? Well, quit it! Sheesh! Gimme a break, you big Miltank! Heh! See what I did there? A little joke? With the Miltank? Ha ha ha ha ha ha!
You sweat drop as your partner continues laughing.
The partner being a horrible liar. Not long after the partner's introduction, Carracosta shows up and accuses the partner of gorging on Oran Berries from the garden. The partner initially denies this fervently, but when prompted on how they tasted, answers brightly that they were delicious. This is quickly followed by the other villagers, angry at the partner's shenanigans, joining to form a stampede to chase the partner down. Needless to say, the player is left dumbfounded on what just happened.
The entirety of Drilbur Coal Mine.
Before you and your partner enter the Mine, the Drilbur outside quickly tell them it is restricted. The partner then tells the player loudly that they will sneak inside and tells the Drilbur brightly that they will be real sneaky. You and your partner just walk in anyway in the end while the Drilbur just remained looking away from them.
In the part where you and your partner are about to go deeper through the barricaded path, your partner tells the Drilbur to "look into their eyes and see how serious they are". The Drilbur says he "doesn't see anything", and it becomes even funnier if your partner is, say, a Cyndaquil. This speaks for itself.
Watchog displays what an emera looks like by "projected an image into [the students] young minds", and everyone begins gushing over how amazing that—
Much like the Cyndaquil example above, there is another scene that is amusing if you (or your partner) is a Riolu. In it, your partner asks you to be your friend, and you (in your thoughts) ask your partner if it is a little bit blunt, and why it sounds like an order. Your partner tells you that (obviously) nobody believes anything you have to say right now. You reply with this:
You: (Wow, no punches pulled there...)
When Magnezone and others demonstrate an alliance on Watchog, Magnezone says this:
Magnezone: Take this! Our perfected... "Triple Shock Attack!" (Which we just named right now.)
Espurr flattering Watchog telepathically, distracting him enough so you and your partner can sneak in late to class. Doubles as a Heartwarming Moment, because she felt bad about not accompanying you to save Budew the day before.
After the end of the maingame, Krookodile becomes a milk delivery man and developes a crush on his boss, Miltank.
Let's consider the times you meet the Expedition Society: The first time you meet the Leader (you didn't know who he was at the time) he's fumbling and bumbling through town having no clue where he was going. Then you meet the rest of the members (sans Mawile) who are chasing the Cook for eating all of their food, and then they promptly fall on their stomachs out of hunger, until you and your partner go and get them some food. Our heroes ladies and gentlemen!
In their chase for their cook, they end up breaking the Pokemon Nexus on accident. This is implied to have happened multiple times, much to the chagrin of Archen.
If you look closely at Ampharos's character sprite when he's stumbling around, he appears to have his eyes closed, meaning his No Sense of Direction is at least partially intentional for Arceus knows what reason.
Shortly after this, your partner quickly realizes that since the both of you ditched class the previous day (to save Budew, but still) you're both in for one heck of a lecture and suggest that you skip school today to avoid it. Your character's only response is a hard stare that lasts for a few seconds and your partner concedes that they should just face the music and go to school. The absolute funniest thing, though, is Kecleon nearby silently listening to the two of you, as he turns towards the two of you when your partner says something about ditching school and then turns back and nods his head when the two of you ultimately decide to go anyway.
After you and your partner join the Expedition Society as Junior members, your partner gets all determined and starts to act brave and bold...and you end up sweat dropping in response.
After your first night at the Expedition Society Headquarters, you and your partner are pulled into a sudden fight by Jirachi... because you happened to be trying to wake him up and stood in the wrong place (right as he told you that he sometimes attacked people standing in front of him while he sleeps). The entire fight is fought with Jirachi still asleep, and his cheerful introduction afterwards says volumes.
The fact that he says the exact same things to Bidoof in Explorers of Sky makes it funnier. He never learns.
At the end, just after defeating the Dark Matter for good, everyone meets up with you. Jirachi and Ampharos do not hug. They body slam! (by accident, too!)
Made even funnier when you (successfully) dodge their body slams and your partner (hilarious) can't avoid Ampharos'.
...and after getting hit by Ampharos, the partner plays dead to avoid getting another body slam. Even Ampharos thinks he may have seriously injured or killed the partner!
When you 'recruit' Hoopa, he lampshades that the connected scene doesn't occur, since he doesn't join your team permanently. So he decides to take matters into his own hands...
Hoopa: Now...we're..CONNECTED!
After a heartwarming scene of you and your partner becoming Junior Expedition Society members, a few seconds later, Dedenne contacts Ampharos and, after a while, then chews out Ampharos for getting lost due to his horrible sense of direction.
After Jirachi tells the Expedition Society that you were a human, Dedenne, Bunnelby, Buizel and Archen appear to be shocked by the news...then almost immediately after, they go on eating as if nothing had happened.
After the explanation sinks in, the Society treats it like it's no big deal.
In other Pokemon Mystery Dungeon games, the move Splash caused the user to jump in a random direction, causing Scratch Damage at best. In this game?
Description: Your flopping efforts finally pay off. You jump over an enemy or a teammate and get behind it.
While it's also very annoying when it happens to your Pokemon, there's something hilarious about how a confused Pokemon will drunkenly shoot its attacks in random directions.
Like everyone else in Serene Village, Hawlucha's urging the protagonists to stay safe and not leave town, but with Professional Wrestling flavor thrown in:
Hawlucha: "It's too soon for you cute kids... to go leaping from the top rope! Take it easy!"
After you and your partner sneak off to stop some ghosts, Pancham and Shelmet are saved, and everyone sneaks back home unnoticed... But you and your partner get scolded by Carracosta for sneaking off without permission, despite Nuzleaf trying to explain to Carracosta that there is no reason to scold you and your partner, but Carracosta tells Nuzleaf to step up to the task. It is at this point that your partner decides that they're bushed and falls asleep, complete with Catching Some Z's. Though, to be fair, it took all of their strength and willpower to face their fear of ghosts before returning home, so you have to feel for them. Regardless, despite Carracosta yelling at your partner to wake up, your partner is still snoring away. As a result, Carracosta turns to you and tells you that you alone are left to take the scolding, much to your horror. What happens next is priceless, with Carracosta's scolding consisting of *nag* and *gripe*. The story text then explains what happens next.
And so, {player name}...ended up on the receiving end of one of Carracosta's infamous lectures...unable to escape until nearly dawn, and all in {partner name}'s place.
Fortunately (?) for the protagonist's sake, the partner doesn't escape further punishment. Carracosta grounds the partner and makes them clean the house all day, the next day, leaving you to go out on missions yourself.
Partner: "Ok pops, I'm done cleaning this part!"
Carracosta: "DOES THIS LOOK CLEAN TO YOU!?"
As an aside, there's something amusing about the fact that Nuzleaf (who has a type advantage and is a servant of Dark Matter) is visibly afraid of Carracosta. Nothing scarier than a worriedparent.
When Ampharos is about to save you from Nuzleaf and his pack, he greets them with this gem:
Ampharos: It's a pleasure to meet you... Oh wait. No, it's not.
There's also this:
Ampharos: Bingo! The Tree of Life isn't dead yet! It's still alive and kicking!
Jirachi: There's still hope! As an aside, Ampharos, trees don't kick.
Similar to the aforementioned first exchange with your partner, there's also the first exchange with Mew. When you explain why you came looking for Mew in the first place:
Mew: You mean this {partner name} of yours was- And way back in the ancient past, I-
Mew: Yeah, you know what? I... The truth is, I... I've got no idea what you're talking about!
You are shocked by this.
Mew: Ahahahahaha!!
You sweat drop as Mew continues laughing.
This is later followed by Mew asking if you are leaving before stalking you. Your reactions range from sweat dropping to becoming nervous before you turn around to realize that Mew is following you back to the Expedition Society.
This exchange during the epilogue:
Dedenne: I'm glad to have a new member! Plus, Mythical Pokémon are super rare!
Jirachi: Um...you do remember that you've already got one Mythical Pokémon right here? Here I am, flying, right here?
A game mechanic example, the new way Unown work in this game. Simply bringing one to a mission gives your whole party a massive Exp multiplier, which stacks with the "Motivated Bonus" so Motivated Unown can end up giving as much 6 times experience. The developers were clearly aware of how incredibly bad Unown is (and how much it would suck to get as your motivated Pokemon for the day) and knew they had to give players a massive reward for actually using one.
Just before the boss fight at Poliwrath River, the partner reckons that a two vs three fight isn't too bad, only for the Poliwrath to summon their minions... who turn out to be exactly one Poliwag.
Similarly, just before the fight with Gabite, he summons his Drilbur minions to aid him... only for all of them to tell him that they really don't want to fight and unceremoniously leave.
Due to some Artificial Stupidity, sometimes missions seem to solve themselves: for example, fainted Pokemon (who need to be given an Apple to be revived) can be found very close to or on top of Apples. In addition, the only non-fixed message mission is randomly spawned, meaning that on occasion, Gallade will ask you to take the message to Roserade, who could be anywhere... and Roserade might be standing right across the room.
While the whole deal about Pokemon being turned into stone is no laughing matter, it gets a minor funny moment when it's revealed that Swirlix faced the same fate... while she was eating Perfect Apples.
Immediately after, when you and your partner metaphorically kick the door down into the Expedition Society Headquarters, it's revealed that the shopkeeps Kecleom, Cofagrigus, Klefki and Hawlucha all escaped being Taken for Granite. Unfortunately, you scare them so much, Hawlucha retreats to your room and is left peeking around the doorframe.
Sometimes, the messages you get after completing missions are this. One is about giving a fainted Zweilous an apple. Since Zweilous is a two-headed Pokemon, what happens? One of the heads complains about not getting the apple while the other did.
After a major plot twist, the player is treated to the sobering sight of the player, partner, and most of the Expedition society turned to stone. Afterwards, the screen fades to black, and what does the game tell you?
Game: You've had a great adventure today!
Play Nintendo extra videos
A Day in the Life of My Old Pops
When Carracosta finishes cooking his food, he inexplicably imagines Buizel being knocked out by Entei... just as the kitchen timer stops:
Carracosta:(Cheerfully) Bon appetit! (Shocked) ... Wait, what? What is this thing!? Where did this image come from!? (Angry) Begone, foul fantasy! (The image vanishes) Wh-where did that awful image come from? Not... not from my imagination! Perhaps I'm more tired than I thought.
That being said, his imagination of a Buizel defeated by a Fire-type Pokemon, calling it a "foul fantasy" and hoping it was not his imagination can be Fridge Horror if you think of it hard enough...
Ampharos's atrocious attempts to hide the fact he and Swirlix ate Carracosta's food:
Ampharos: Oh. Good evening! Ampharos at your service. It certainly has been ages since I last made it to Serene Village. We were wandering by when we smelled the most delicious of smells! (Happy) We let ourselves in, and- can you believe it? We found an amazing spread right before us! Now I'll have you know that Swirlix and myself were starving on our feet, too. But then... something mysterious happened. We'd hardly stepped in the door when all the food disappeared! (Puzzled) All that delicious-tasting food... I mean, all that delicious-LOOKING food... I wonder where in the world it could have gone? Carracosta:(Shaking) You... You! Ampharos: We? Carracosta:(Pissed Off) You... youFOOLS! And so it was that Carracosta ended up losing his temper again that night, like any other night...
It's Your Store Now
We see that it is not so easy to be a store keeper of Kecleon's shop, being pulled everywhere from different directions. Even more amusing by the fact that when the heroes go to see Kecleon, they are the only customers.
Cofagrigus is as hammy as ever, by laughing maniacally at the rookie Kecleon's naïveté of what being a store owner is truly like.
Later on, while him buying Kecleon a beverage is heartwarming on it's own, his hamminess still makes it hilarious.
Pokémon Friendship
The female Jellicent prying onto Umbreon and Espeon's bond between each other after Quagsire sent them in his stead. When she brought up the Glacier Palace, Espeon first thinks that it is more grim than romantic... Before realizing how she could have known that, especially when it was the two of them.
Umbreon stalls for the interview to run out of time wisely by slowly stating that the Jellicent can understand their bond with the Connection Orb.
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