Pokémon Diamond and Pearl has several references to Something Awful as a result of Nob Ogasawara, one of the series' lead translators, frequenting the forums under the pseudonym Douglas Dinsdale. For example, a female trainer with a Wooper is named "Roxy" after the name chosen for the main character of Chorocojo's Let's Play of Pokémon Crystal that decided to get rid of her Totodile because it was evil, and replaced it with a Wooper. Also, after you fight an Artist trainer, he tells you he's been inspired to paint a picture called "My Pokémon is Fight!", a reference to Zack Parson's book My Tank Is Fight!
The references are still there for Pokémon Black and White: In that Let's Play from Crystal, Roxy finds a Pikachu and names it Gesundheit. The only non-Unova Pokémon before the National Pokédex is a NPC Pikachu in Castelia City, more specifically in the Name Rater's house. The name? Gesundheit.
Nob Ogasawara has actually been part of the translation teams of the franchise from the beginning to Platinum, but Diamond and Pearl was the first time he actually started putting memes into the translation.
At Dragonspiral Tower, as you get closer to the top, you can hear things going crazy and someone is shouting "Burn, baby, burn!"
There is also an old lady who tells the player character that she doesn't have any stairs in her house, a Shout-Out to an IRC prank-cum-sign/countersign which was popular on the forums for a while.
In Diamond and Pearl the receptionist at the Team Galactic HQ exclaims "Cosmic energy for the win!"
The Pokémon series in general, but Diamond and Pearl especially, reference the also-developed-by-Game Freak Pulseman. The St. Anne (English's S.S. Anne), Volt Tackle (named for Volteccer, which was in turn named for Voltekka), and even the main villains of Diamond and Pearl are shout outs, as is the Pokémon Rotom. There's also that one point in the original games where, upon viewing an SNES console, you're told it's a game featuring Mario with a bucket on his head.
Beauty Nevah in XD has a Cacnea and a Chimecho on her team, and her introduction speech says that there's someone else out there with those two Pokémon. That statement isn't true anymore, but since this was a Generation III game, she was talking about James.
Gold and Silver has Earl, the strangely-speaking Pokémon teacher in Violet City, asking "want to be a winner is you?". HeartGold and SoulSilver, meanwhile has your rival ask "Why so serious?" when sending out his last Pokémon.
In the French localization of Crystal, the three Sages that test your worthiness to enter the Tin Tower are named Ken, Shuu, and Raoh.
In the French version of Pokémon Gold and Silver, a NPC trainer near Tohjo Falls will say, after being defeated: "Enfant du Soleil, tu parcours la terre le ciel, cherche ton chemin, c'est ta vie c'est ton destin". Those are the first lines of the French version of The Mysterious Cities of Gold's opening song.
MOTHER shout outs are a recurring trend in the series, with examples present as far back as the original Red and Blue. The involvement of Creatures, Inc. on the series may have something to do with it.
Pokémon Black and White hits MOTHER 3 in particular: the Waitress trainer class bears a strong resemblance to Tazmily villager Tessie, Drilbur (who strongly resembles the Mischievous Mole enemy) evolves into Excadrill (a mole with drill hands like Reconstructed Mole), there is a Dark/Dragon line, and the song "N's Farewell" contains note for note a portion of the Mother 3 Love Theme, as well as fragments of "Letter to You, My Sweet."
HeartGold/SoulSilver adopted a quirky self-referential style of humour which reminds one somewhat of the MOTHER series' humour style.
In X and Y, there's a man in a Center remarks about a game he's been playing recently, where you play as a boy that goes around beating up enemies to the beat of music. It also could be referencing HarmoKnight.
The Dark (Evil in Japan) type is weak against Bug and Fighting. Pawniard and Bisharp also bear a good resemblance to tokusatsu heroes.
To build on music references, in Pokémon Black and White 2, the guitarist of Roxie's band is named Billy Jo. The band is also a three member band with a guitarist and a bassist providing vocals. It should be mentioned though, that said guitarist is female.
The Poison-themed Gym featuring a rock band is a bit of a pun referencing the band Poison.
Speaking of Gym Music in B2W2, there's Elesa's Gym theme: when she makes her entrance, and the traditional Gym tune kicks in, you can hear that the soundfont used borrows some vocal bits from "Dancer In The Street"note (Heard when fighting Pig Noise.).
In Generation II and IV, there are three Bug Catchers on Route 2, named Rob, Doug, and Ed.
There are a pair of Bug Catchers, fought as a double battle in Gen IV, who share their names with the Everly Brothers.
In Black and White 2, there are two Black Belts named Rocky and Drago in Seaside Cave, who use Roggenrola and Scrafty, respectively.
One issue of the manga had Gastly, Haunter, and Gengar note one wants to say "Gastlies," "Haunters," and "Gengars" infesting a town and being captured by some Ghostbusters-type characters.
Ghetsis faces down Gym Leader Clay, a sheriff strongly reminiscent of John Wayne, with a small army to demand the return of his imprisoned gang members. That's the plot of the John Wayne classic Rio Bravo.
Generation V introduced a move called Smack Down. It's Rock-type, of course.
In Crystal, there is a trio of sages that you must fight to reach the Bell Tower. Their names in the French localization are Ken, Shuu, and Raoh.
Pokémon X and Y seem like they may have been designed with The Hunchback of Notre Dame in mind, both the original and the Disney version. Along with the France-based setting and the "beauty" theme, there's also a tragic, deformed giant heavily involved with a loved one, a genocidal Anti-Villain who is also tragic but nonetheless believes in mass extermination for the greater goodnote which is closer to the original Frollo than the Disney version, and closing credits set to an Award Bait Song and a parchment-like backgroundnote lifted straight from the Disney version... all that's missing is the "parental abuse" subplotnote which was already covered in Black and White and an analogue to the Notre Dame cathedral itself.
The Kalos Pokémon League is very cathedral-like in structure. Makes sense, as the final battles are fought there.
New Pokemon Sylveon has blue eyes, odango-like ribbons, and has the moon as a background as well as a moonlight-based damaging move. Sound familiar?
Similarly, Mega Diancie from Omega Ruby and Alpha Sapphire bears an uncanny resemblance to Goddess Madoka - which is even more "unseeable" than the Sylveon/Kyubey comparisons.
The first gym's gimmick is you being forced to traverse a gigantic spider web. The last trainer you fight just before reaching Viola is a Lass named Charlotte. Speaking of the Gym Leader at the end of the spider web, Viola is a photographer.
Xerneas shares similarities with The Spirit Of The Forest from the film Princess Mononoke. Both resemble deer-like creatures with elaborate antlers. Both are associated with the ability to bring life. And, both are considered powerful creatures of legend in both their respective franchises.
One of the people in the Furfrou fanciers' cafe in Lumiose City mentions that he gives a good-bye kiss to each of his Furfrou before heading to work. All 101 of them.
After defeating the first trainer on Route 10, he will respond with: "Wow! You and your Pokemon's power levels are incredible! They're over 9,000 for sure!"
Once you will defeat a certain Preschooler on Route 4, she will say "Hey! Hey! Listen!"
One of the Flavor Texts for Super Training in X and Y is "Float like a Butterfree, sting like a Beedrill", a reference to Muhammed Ali's famous quote, "Float like a butterfly, sting like a bee," which was often his strategy during boxing, besides the Rope-a-Dope. Remember - you can't hit what you can't see.
In X and Y, on Route 15, you can find a Hex Maniac standing in front of a ruined building. What's her name? Carrie.
And she has a Litwick in her team, another nod to the book.
One of the battlers in the Battle Tower is named Bug Catcher Tajiri. The creator of Pokemon is Satoshi Tajiri, who says that he based Pokemon on his childhood pastime of bug catching.
At the Village Bridge in Pokemon Black 2 and Pokemon White 2, you can find an Artist named Gough, whose only Pokemon is a Sunflora. The reference is made more blatant in Japanese, where his name is Vincent.
Four of the Fairy Tale Girls at the Battle Maison in X and Y are named after female characters from French fairy tales (Kalos being based on France). There's Aurore (Sleeping Beauty's daughter's name in the original Perrault version and Sleeping Beauty herself's name in the ballet version), Abricotine (a fairy princess in The Imp Prince by Madame d'Aulnoy), Blondine (Princess Belle-Etoile's mother in Princess Belle-Etoile, also by Madame d'Aulnoy), and Rosanella (the protagonist of a fairy tale by the same name by the Comte de Caylus).
Primal Groudon and Primal Kyogre's "Primal Reversion" transformation was triggered in the past by absorbing massive amounts of "nature's energy", which gave them a massive increase in power, in addition to unique markings and physical transformations to their body. Sounds like Groudon and Kyogre were the first to use Sage Mode.
Fire Blast explodes in the shape of, and in the Japanese version is named after, the Daimonji, the climax of the Japanese Bon Festival.
Cyrus's goal was to create a universe where emotions were a thing of the past because they caused violence, where logic and order were the rule, and, looking at his followers, where bowlcuts are as far as the eye can see. Combine that with the overall space/sci-fi look of Team Galactic and his inspiration seems obvious.
The two characters of the day in the 99th episode of the Best Wishes series of the anime, Soren and Rocko, are named Sora(n) and Riku in the Japanese dub.
A Diamond and Pearl character of the day, Jeffrey, even has a hairstyle similar to Sora's.
In episode 14 of X and Y Serena becomes convinced the mansion they're in is alive and eats people. After seeing pictures of an old woman in it she's adds to that theory the woman's ghost is possessing the house. Both of these are references to the film Monster House, with Serena's imagine spot even looking like the titular house in the film.