When the player first encounters Team Plasma, the Plasma Grunt throws TM21 Frustration at the player and runs away.
Roxie's furious reaction to her father wanting to become a ship captain and a movie star. "You dim-witted...dense...dumb...daft...dippy...dorky...doltish DOOFUS!!!"
Speaking of her, Gym Leaders always give you relatively long introductory speeches regarding their Pokémon preference and how they view fighting and living with Pokémon. Roxie's ? "Get ready! I'm gonna knock some sense outta ya!" ...and that's it. It's a really funny departure from the usual tradition.
Nursery Aide Rosalyn in Pinwheel Forest. "Hear the cry of my heart! Everyone SIT DOWN and SHUT UP!"
Asking Brycenman if he is looking for the bathroom in the first "Brycenman Returns" movie (twice, both times in denial).
If you're playing as a girl, and knock out Brycenman's Pokémon, while Brycenman talks about the amazing power of the black diamond, she starts to giggle, and think that with its power, she can become even cuter, and leaves Brycenman behind to head after the cruise ship.
In Invaders 2, the Strange Ending involves getting a crushing debt of a billion Pokédollars from over-doing things and destroying the UFO (read: using a damaging move other than Zap Cannon), requiring you to be E's assistant for all time. It's made even funnier if you use something like a level 80 something pseudo-legendary against the level 38 UFO, even when it's revealed E is an alien in a later film.
"Mystery Doors"'s first weird ending has you leaving to find someone to "train" with, and causes the evil queen to not want you as her servant.
The second is rather weird in that you become a door. Of course, it borders more on Nightmare Fuel in the implications, but still...
The last one in the series has the character (at least if they are male) falling in love with the queen (who is 108 years old). Even better, she agrees (somewhat, doubles as heartwarming because she doesn't steal the life essence and actually does marry the character).
In Love And Battles, the protagonist falls in love with the Ace Trainer's Smeargle and creeps both the Smeargle and the Ace Trainer, made funnier if the Smeargle runs out of PP on Guillotine. Oh, and since the Smeargle is always a guy regardless, bonus points if you play as Nate for the Ho Yay factor added in.
The Strange Ending to the first three Ghost Eraser films being that the hauntings were fake and a publicity stunt to get revenue and popularity for the town. The first was funny in how the character is pissed off and the second more so in that they fall for it again. It makes it appear as if the town was trolling the Erasers that time. By the third one, the Eraser is clearly flustered at being screwed with and the "Gulp" from the client sealed it.
One of the Plasma Grunts mentions that Hugh has hair like a Qwilfish (this comes up several times, actually).
Similarly, another Plasma grunt calls Marlon "smiley swimsuit".
In Humilau City, there is an old woman who will ask you to walk her Mienfoo around her house. If you try to leave, watch TV, or even check her trash bin, she will freak out.
There is a house in Icirrus City that can only be accessed in the wintertime. In that house, there's a couple who consists of a Roughneck who was formerly a member of Team Magma, and a Pokémon Ranger who was formerly a member of Team Aqua. They both tell you not to tell the other.
After beating Marlon, he jumps in the water behind him and swims off underwater. And the top of his hair sticks up like a periscope.
Apparently, Clyde the Gym Guide is aware of this.
Clyde: Marlon's swimming around, isn't he...
Remember the "Go! Hyper Beam!" toddler at the Daycare in the first games? He's still there and says it again before challenging you. Then, if you talk to him after beating him, he says that none of his Pokémon know it, and that "Maybe I should unleash a Giga Impact instead?"
There is, however, a Youngster who rants about his shorts in the Pinwheel Forest.
A man on the Skyarrow Bridge tries to get you to buy a Fresh Water from him for $300 (as compared to $200 from the vending machines). If you say no, he'll try even harder to sell it to you, and you'll have to say no again. If you ask him again and say no once more, he'll come up with a different excuse. It can be funny to see what he has to say.
Route 2, in general, which has a bunch of trainers with derpy Pokémon. Two trainers with different Bug-type Pokémon, a Youngster with all five "derps"note the Normal-types that every generation introduces that you see at the beginning of the game, like Rattata and Bidoof. Then a Lass with all five Flying-type derps like Pidgey and Starly. And if you talk to the derp Youngster after beating him, he refers to the trainer from the original Black and White and how he's been training ever since.
Relatedly, that entire part of the map is inordinately hilarious due to the Sorting Algorithm of Evil. The first section of the map from the first Black and White is inaccessible until the postgame due to bridge maintenance, but hasn't actually changed all that much in terms of resident trainers and Pokémon - only the levels have changed to match that which the player can be expected to be at after beating the Champion. So, it's absolutely full of small children, schoolteachers, and assorted other random average Joes who happen to have largely-unevolved Com Mons overleveled enough to wipe the floor with all eight gym leaders.
There's always a Poké Mart employee at the first route to give you a free potion and the one from Black and White is still there at route 1 in Black 2 and White 2... and just like two years before, she gives you a free potion sample, even if you are surrounded by trainers with Pokémon that deal a lot more damage than a single potion can heal.
You can try to walk away from battling the Champion after the lights in the final room turn on. Doing makes the Champion exclaim, "Whaa?! Where are you going?"
One of the basketball players who appears in the Small Court on some days, when you beat him in the post-game, says, "UGH!!! I missed the basket! I was blocked!" Then, he says, "I'm gonna throw this item, so you'd better block it!" and you get a Calcium. In fact, a lot of the quotes that these athletes have to say are rather amusing.
If you try to access the room Ghetsis is in before beating Colress, a Team Plasma grunt will refuse to let you pass, telling you that you have to beat Colress (who the grunt expects to wipe the floor with you) before you can do so. After you've beaten him, the grunt, shocked, admits that he pretended to be strong, but doesn't have any Pokémon, and runs off like a coward.
If you unlocked the Memory Link, there is the conversation between Elesa and Skyla. Elesa is basically invoking the Pungeon Master to change her image, but falls right into Adorkable instead. The amusing bit? Skyla, the Gym Leader whose Gym is a gigantic safety hazard in both the first game and sequel, comes off as the straight man in the discussion!
Even better if you didn't do many Musicals in your previous file... The director will still go on about how awesome Hilbert/Hilda was, but then Fridge Logic will kick in.
Lass Persephone's Ferris wheel date with Nate in Spring. She'll start off ridiculously harsh, calling herself the "Feral Liepard," then tries to get Nate to freak out over the Ferris wheel... only to get scared herself on the way down. She then gets all sulky and tells you not to tell anyone.
In the third part of "Mystery Doors to the Magical Land", if you play as Rosa, you can get into a lengthy argument with Queen Bellelba over which one of you is the cutest in what is supposed to be a fight for your freedom. Possibly even more amusing when you realize that Queen Bellelba is played by Sabrina and she just rolls with it when you decide to turn the whole thing into a joke.
If you play as Nate, she'll ask you to give up already because she wants to go home and take her makeup off.
On a related note, any time Brycen decides to just roll with it if you go for a strange ending in any of his movies.
Some of the medals!
Magikarp Award: A medal to praise the guts of Trainers who kept using Splash no matter what.
Trash Master: A medal for curiosity seekers who checked trash cans even though they knew they were empty.
Noneffective Artist: A consolation medal for Trainers who made the cute mistake of using noneffective moves.