Pokémon Diamond and Pearl has several references to Something Awful as a result of the translator, Nob Ogasawara, 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 a 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.
"Galactic Energy For The Win!"
The Pokémon series in general, but Diamond and Pearl especially, reference the also-developed-by-GameFreak Pulseman, which never saw release outside of Japan is now out on Virtual Console. 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 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 somewhat of the MOTHER series' humour style.
It gets better. The first time you transfer Pokemon, the Professor says "Well, let's begin. Allons-y!" After you're done: Great! Molto Bene!
In Pokemon Diamond and Pearl, you fight a trainer named Kirby. He has one Cleffa on his team, a species generally known as the "Star Shape Pokemon." It's also pink, small, and cute.
Several Pokemon are based off of various Kaiju from the Toho films.
Both Feraligatr and Tyranitar are based off of Godzilla.
Nidoking and Nidoqueen are based off of Baragon. This is because Baragon is very popular in Japan and has made cameos in several shows and video games.
Hydreigon is based off of King Ghidorah. His Japanese name "Sazandora" is a reference to the name "King Ghidorah".