In the Mistralton (sixth) Gym, you have to navigate through a series of cannons that blast you into the air, in order to reach the Gym Leader. One of the cannons "accidentally" blasts you out too far... and your character ends up face planting into the nearby wall.
The first battle in the game, when you receive your first Pokémon as a present. After the battle, the game returns to the player's bedroom... And the place is totaled, with the bed a mess and footprints everywhere. Even on the walls.
It becomes even funnier when you realize that, after your battle with Cynthia in Undella Town, the house is unscratched.
And funnier still when you realize that you have plenty of indoor battles in every game in the series, and yet nothing bad happens to whatever building you were in... So it makes one wonder exactly how crazy you and Bianca must have gotten with your little level 5 starters.
The "idle" animation for Scraggy in battle - it picks up its "pants" (actually skin shed to look like pants), then lets go of them, as if to say, "Look at me! No hands!"... but then the pants sag back down to normal anyway. Funny and adorable!
Palpitoad's in-battle animation involves it doing some sort of... shaky-seizure wriggle thingy, along with a really funky cry.
In Castelia City, after Team Plasma steals Bianca's Munna, Burgh begins to say that finding any specific person in a place that big will be like finding a needle in a haystack. Then the Team Plasma member walks right up to you and quickly runs away.
In Castelia City, an NPC has a Pikachu named Gesundheit.
"This is bad! Badbadbadbadbadbadbad! Bad for Team Plasma! Or Plasbad for short!"
Team Plasma's battle quotes can actually be pretty funny.
"Here I come!"
Even funnier if you speak Dutch: "Plasbad" can be literally translated into English as "pee-bath".
What Reshiram's roar is translated as when it awakes. "Burn Baby Burn!"
And when it's Zekrom in Black Version, the line is, "That's electrifying!"
When you pull up the case where your Badges are kept, there are little portraits of each of the Gym Leaders above it. When you select one, it shows their name, what city they're from, and a quote. Lenora's? "Curiosity is the spice of life! Without it, life is bland!" Elesa's? "May you always continue to be a person who brightens your surroundings." Burgh's? "Umm... That's right. You! Use Bug-type Pokemon!"
In battle against a Stunfisk, sometimes it gets this odd expression strangely similar to the "Awesome Face" meme on its face that makes it look like its giggling to itself. Seriously, Stunfisk might as well have its Pokédex classification changed to "the Meme Pokémon."
Of course its true classification (the Trap Pokémon) can be nearly as hilarious when the first one you catch is female.
And that its cry sounds like a fart and then it smiles. There's also Black's Pokedex descriptions.
The eyes of Swellow looks like the one of the "what" meme faces.
"The way it works is blah blah... radioactive energy blah blah... blah blah blah infrared technology... blah blah blah..."
What's funnier about the chap who says "blah blah blah" implies that the player character just flat-out stopped listening to him entirely, tuning in every so often to see if he was quite done yet, and on realising he was still rambling with no end in sight, just went back to not listening. Heck, the entire scene is funny, because you walk in, are promptly kidnapped by a scientist after she learns you have all 8 badges (the way the scene is played out, it's easy to imagine she just grabbed you by the arm and dragged you upstairs, cheerfully shouting about how you obtained all 8 badges), and it's somehow funnier since the protagonist is a Silent Hero.
On your first visit, the scientist who explains the mechanics of the Poke Transfer tells the Poke Transfer's creator that you have "all the badges. All ofthem!"
By now, everyone's heard of the "Dennis" Mondegreen regarding Ghetsis' battle theme. However, it gets infinitely more hilarious if you speak Swedish:note In Swedish, "penis" is pronounced "'pɛːnɪs". IPA pronounciation guide here.
The French version of the ferris wheel date with the waitress (if you're playing the female character)... seems to be a mix of the Japanese and American versions: first she spews out romantic stuff about two people on a beach (it sounds like it's her and you); then she mentions someone going back to Johto, leaving her behind; then she quotes a famous French song except replacing the name of the song with the name of the one who abandoned her... that is, her Lickilicky.
Pokémon Musicals. Have your most terrifying Pokémon compete. Watch them dance around on a stage. Dressed like Santa Claus.
Take your Zekrom or Hydreigon. Enter it into the musical, and put it into the Exciting Nimbasa category, which is mostly watched by kids. Hilarity Ensues.
Put Kyurem in. It's hilarious. Or, go for evolved Pokémon - or just plain weird ones — like Volcarona, Sigilyph, or Archeops. Compare them to the (usually) unevolved Pokémon alongside them. As entertainment goes, it's good. (That and watching them spin stupid props around. And wearing them.)
On Friday nights, a motorcycle gang called the Black Empoleon takes over Tubeline Bridge. After you kick their leader's butt, he renames their gang in honor of your lead Pokémon. Needless to say, some of the results can cross into this. Such a massive biker gang being called "Black Lillipup" deserves some chuckles. Or, if you feel that you want to make their already reduced credibility go down even further, in the post-game, it is possible to confront them with a Magikarp as your lead Pokémon. "Black Magikarp" indeed.
It gets better if it's Reshiram or Zekrom. Black Zekrom makes sense; Black Reshiram, not so much.
Immediately after the credits, you meet Looker. He asks you to help him arrest the Seven Sages, then gives you the Super Rod. When your mom asks him what the Super Rod has to do with catching criminals he (after a long string of compliments) explains that the Super Rod...has nothing to do with catching criminals.
Before that, when he first appears he's convincingly disguised as the PC's Mom...while Mom is still in the room, making it look like she's talking to a clone of herself.
If your starter was Oshawott, then the Striaton Gym battle can count — you're up against Cilan, who acts very meek. His reaction the first time you damage his Pokemon without KOing it — even if it was a pitiful blow — contrasts greatly with Cress's dismissive and Chili's mocking lines:
"Ah! My Pokemon!"
His commentary upon being defeated counts too:
"Er... is it over now?"
You wouldn't expect it, but several NPCs' reactions to Team Plasma stealing the Dragon Skull border on being absolutely hysterical — perhaps to make up for the misery that the game has just put you through.
On Route 7, there's some wood planks over the grass. You have to be very careful, or else you'll fall off. If you stand still on the planks, Hilbert/Hilda/Nate/Rosa has a hilarious animation of trying to keep their balance.