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 since the beginning, 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 (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.
The player's TV in other games also references real-life movies, such as Big and Stand by Me.
Registeel, a Steel-type Golem like Legendary Pokémon has a cry that sounds a bit like the Transformation sound.
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.
HeartGold and SoulSilver seem to continue the tradition of Shout Outs with the strangely speaking Pokémon teacher in Violet City saying "A winner is you!". Also, during a battle with your rival, when he sends out his last Pokémon, he'll ask "Why so serious?"
Believe it or not, the A Winner Is You reference has been there ever since the Generation II games!
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."
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.
Hitmonchan's National Pokémon number is 107. That number just happens to be the weight of Little Mac, another Nintendo boxer.
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.
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!"
That in itself is 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.
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.