This show is full of stuff like this. During the episodes featuring Dynamo, it malfunctions and instead of traveling through time, it travels to other dimensions. One of the ones they visit is the original Powerpuff girls.
One episode featured a remake of the Mojo Jojo battle from the original (unreleased on DVD to this day) Tokyo Anime Fair pilot from 2005. One of the girls even wonders if Mojo's robot looks familiar.
Another episode of Splash Star had Saki almost use Nagisa's Catch Phrase, leaving other characters confused for a moment.
And Fresh Pretty Cure!'s fifth episode had five girls in colorful outfits, who looked a lot like the heroines from the previous season, only their color schemes were swapped. In fact, they had done this a couple of times, even putting some of the girls' names on magazine covers in episode 9 and some hairstyles from previous seasons popped up during episode 12.
Heartcatch Precure had inspiring mangaka Ban imagine himself wearing Cure Rouge's GO!GO! outfit.
Mai-Otome has several of these in regards to predecessor series Mai-HiME. A few examples:
Princess/Queen Mashiro lives in a place called "Fuuka Palace". In Mai-HiME, Mashiro was the acting headmaster of Fuuka Academy, the main setting for that show. Additionally, the central setting for the first half of Mai-Otome is The Kingdom of Windbloom, while "fuuka" is written in Japanese with the characters for "wind" and "flower".
The name "Windbloom", in fact, is also a reference to HiME Mashiro's surname, Kazahana, which also means "wind flower". Some other characters, like Akane and Yukino, also have surnames that are "Westernized" versions of those of their Mai-HiME counterparts.
Mikoto, a Big EaterGenki Girl with a fondness for running on all fours like a cat, shows up as two similarly-named characters. One is an actual cat with a tendency to eat anything in sight, and the other as an ethereal goddess and protector of the Harmonium Organ with a shadowy form that looks a lot like HiME!Mikoto's "beast mode", complete with Glowing Eyes of Doom. One of Cat!Mikoto's favorite foods is rumored to be "Tokiha mushrooms". HiME!Mikoto was a big fan of Mai Tokiha's cooking.
In Human!Mikoto's first appearance, she has a fireball-shaped tattoo on her arm that directly resembles the HiME logo.
In the manga, they're sort of merged into a single being, who happens to be not as nice as she first seemed.
Four of the Meister Otomes (Natsuki, Shizuru, Haruka and Mai) all know each other from their Garderobe academy days, and Natsuki and Mai met Yukino, who was a student at Windbloom University and a friend of Haruka's, around that time. Their HiME counterparts were all students at Fuuka Academy at around the same time. Haruka even complains about Shizuru "making her do all the work" during their survival test, a similar complaint that HiME!Haruka made toward HiME!Shizuru when the latter ran the Absurdly Powerful Student Council.
The manga makes a Shout-Out to a gag from the Mai-Hime manga: Haruka is eating from a cup of ramen labeled "E-Cup". In the Hime manga, Mikoto grabs Mai's chest and notes that she's an E-cup. In both cases, the text format is exactly the same.
Shizuru also notes that Mai is an E or F cup in the sound drama "Lingerie Rhapsody".
Arika decides to call her mysterious patron "Sir" because Nao told her that it's what older men like to be called. Guess what HiME!Nao did in her spare time?
In the sound dramas, Mai, calling Natsuki "Kruger-san" during their early days at Garderobe, notes that her last name is difficult to pronounce, and suggests calling her "Kuga-san" instead, which was her surname in Mai-HiME. Similarly, Haruka's land ship, the Suzushiro, is named after her surname in Mai-HiME and Nao's Embarrassing First Name, Juliet, is based off the name of her Child.
In Mai-Otome 0~S.ifr~, Lena adopts the alias "Lena Yumemiya" while traveling, which is appropriate considering that she's Arika's mother. A cat called "Nina", whom Arika and Erstin found and returned to the Nina lookalike from Mai-HiME in the Mai-Otome picture drama, appears midway through Episode 1.
The Best Wishes series has one in the first episode!
Also in the first episode of Black and White: the plane Ash takes to Unova is flight number 151.
Black and White also has episode 6's classic "ding-ding-ding-a-ding!" chime when healing Pokémon in the games.
In DP 094, "Doc Brock", a Zapdos makes a quick cameo. In Pokémon Platinum, Zapdos can be found roaming Sinnoh in the post-Elite Four storyline. Notably, this was the first episode to air in Japan after the release of Platinum.
Repeated in DP 142, "Where No Togepi Has Gone Before", where the evil Killer Rabbit Togepi knows Extrasensory. In Japan, this was the last episode to air before the release of Pokémon Heart Gold and Soul Silver. In those games, guess which move Togepi can use for the first time?
In "Ya See we Want an Evolution!", the organization dedicated to showing the strength of Pokémon without evolving them is called the "B-Button League", referring to the actual game mechanic used for the very same purpose.
During a fantasy Team Rocket is having over possibly finding treasure in BW 135, Meowth references previous games in the series.
In fact, so many are the nods that several fans take the stance that the only aspects of the original game that were changed are those directly contradicted by Nanoha (such as Shiro being alive), with everything else, like Shinobu being a Japanese Vampire, remaining unchanged.
Gundam in general does this quite frequently. Due to the sheer number of entries in the franchise, it's virtually impossible not to make a reference, even by mistake. And this isn't even taking Continuity Nod into account for the Universal Century entries.
The last few episodes of G Gundam feature cameos from past Gundam series, at least one super robot from a non-Gundam series, and the Wing Gundam from the then-unaired (it began after G ended) Gundam Wing.
Gundam Wing has blink-and-you'll-miss-it references in Sandrock's blueprints to "Gundarium Theta" and "ALICE System", the latter an AI from Gundam Sentinel.
Gundam 00 casts the ever-heroic Touru Furuya, the man behind Amuro Ray himself, as Ribbons Almark, the main antagonist. Throw in the fact that he also piloted 0 Gundam... which is basically RX-78 with a different shield and a GN Drive. Late in the series the 0 Gundam is upgraded, which includes being painted in the classic Gundam tricolor, and Ribbons appropriates it when his state-of-the-art Reborns Gundam is crippled.The Movie takes it a step further by revealing that Ribbons' genetic template was a man named E.A. Ray (Ensign Amuro Ray).
Gundam 00 also has the Trans-Am System, which triples the offense, defense and speed of a Gundam while causing it to turn red.
Graham Aker, in the second season, wears a mask, and his Ahead Sakigake is automatically red. when he later gets the Masurao, it is black with red lines on the frame, and the Trans-Am System to make it all red. Both his Masurao and Susanowo are shown to be 3 times faster than any other MS when they deploy for the first time, except for the 00 Raiser, of course.
In the first season of SD Gundam Force, the Dark Axis Big Bad is a Commander Sazabi. Before he actually makes his appearance, however, he sends his right-hand-man Zako Red (a Char Custom Red Zaku) to serve as his herald. When Sazabi finally arrives, Red goes to meet him, only to mysteriously deactivate and get shoved out of the way by his boss. The likely explanation is that Red was just a remote control avatar for Sazabi, a reference to the fact that in the Universal Century, both suits were piloted by Char. The Zaku first, and then Sazabi in Char's Counterattack.
In ∀ Gundam, when the Moonrace comes experiences lightning for the first time, the production staff reused exact dialogue from the original Gundam show, when White Base tried to hide from Ramba Ral inside a thunder cloud.
The melody used in "Turn A Turn" is a backmasked version of the original opening's melody, slowed down a bit, yet not at all improved in sound quality.
The people of Adeska call the Turn A "the White Devil". This is a reference to the original Gundam as well.
And then there's Turn-A's whole Dark History thing, which is pretty much nothing BUT this.
When the characters learn of the Dark History, they see footage from all previous Gundam shows, including a scene where the RX-78-2 Gundam impales a Zaku II with a Beam Saber. Sochie lampshades this by asking if it isn't the White Doll attacking a Borjarnon (which are Zaku IIs (or replicas thereof) that were uncovered and renamed). Someone then points out that the Gundam looks a bit different.
Among the clips shown in the Dark History part, there a clip from the battle 15 years prior to After War Gundam X.
The Core Block System. Seriously. It is a staple in Gundam shows. RX-78 Gundam introduced it, after which every major Gundam show (Counting SEED and SEED Destiny as one) except for Wing, Gundam X and 00 have had at least one Modular Mobile Suit. In order of appearance: Gundam, Guncannon and Guntank, ZZ, V and V2, (Crossbone) X-01, X-02, X-03, Shining Gundam, God Gundam, Turn A, Impulse. And that's just the major series, not including the more than 30 sidestories.
Char Clones. No Gundam without Char Clones. Except for the first show, Z and Char's Counterattack, where there's no Char Clone, as it's the real thing (albeit, in Z, he goes by the name Quattro Bajeena (sometimes mistranslated as Quattro Vagina)).
Gundam AGEhas these in spades. The characters in AGE look suspiciously similar others from other Gundam shows, such as Yurin resembling Tiffa and Woolf resembling Loran. Moreover, in episode 13, Geera Zoi of the UE calls the Diva a Trojan Horse (after seeing it transform into a White Base lookalike).
Mahou Sensei Negima! has a number of these which imply that it takes place in the same universe as Love Hina: Tama the turtle makes a few cameos, Motoko and Setsuna are part of the same sword school, and the character Mei pretty much owes her existence in Negima to this. There's also this which is a direct shout out to a technique used by Motoko Aoyama in Love Hina. (It also helps that the author has confirmed that Motoko and her sister Tsuroko are the two silhouettes seen in one of Setsuna's memories.)
Taken one step further when it's revealed that Tsukuyomi turns out to have the Hina Blade,
Then there's the self-contained ones, like the identity of of the perverted bounty hunter that tried to kidnap Nodoka.
The Negima Summer OAV sneaks a reference to Kotarou by having a picture of his face appear on a fan held by Chizuru, one of the girls that he eventually rooms with once he arrives at Mahora Academy.
In chapter 175 of the manga, when Haruna makes a dark version of Nodoka, one of the notes she writes about Dark Nodoka is that her voice is done by Mamiko Noto, Nodoka's voice actress in the anime version.
Steel Ball Run has several references to the previous series of JoJo's Bizarre Adventure, such as the Speedwagon Oil Co. as a sponsor of the titular race (Robert E. O. Speedwagon, an ally of the first Joestar, Johnathan, hit it big as an oil baron in Texas after the events of Part 1), and there are brief appearances by Alternate Universe versions of Stroheim and Avdol as well.
During Code Geass's first School Festival episode, a student is shown wearing a suit that looks to be halfway between the Lancelot and a Super Sentai costume; this is a nod to Suzaku of the Counterattack, an alternate reality manga, in which the Lancelot is a Kamen Rider-like powersuit rather than a Humongous Mecha. The author's notes for one chapter of Suzaku of the Counterattack even point this out.
In the Lost ColorsVisual Novel, there's a scene where Nunnally fantasizes about being a super-heroine with her own Knightmare Frame; what she describes is the Mark Nemo, the machine she pilots in the Alternate Universe manga Nightmare of Nunnally, complete with a picture of it in the background. Lost Colors also contains a nod to the Nintendo DS RPG by showing primary villains Castor and Pollux on a computer screen.
In Nightmare of Nunally, when Nunally has a vision of alternate realities, that character saw the events from canon Code Geass, including Euphemia massacring the Japanese, Suzaku facing off with Lelouch and Lelouch dying.
The Castle of Cagliostro's more gentlemanly Lupin III reflects back on the wild days of his youth, a time of womanizing, explosions, and not being afraid to use his gun. Y'know, back when he acted like he does everywhere else.
The new pilots in Dancougar Nova repeatedly use variations on Shinobu's catchphrase "Yatte yaruze!" from the original Dancougar, and even fight to be the one who gets to say it first. Finally, near the end of the series, a character played by Shinobu's actor arrives to say the real thing.
Although they are (mostly) unrelated, Studio Ghibli is constantly making references to its other films. For instance:
Lin in Spirited Away comments in an elevator, "You wanna lose your nose?" This line is repeated as a door is about to slam shut on the protagonist of Howl's Moving Castle.
The action in Whisper of the Heart takes place in the exact same area as Pom Poko. In fact, the opening shot of Whisper is the exact same as the last shot of Pom Poko, but urbanized.
The creatures that are briefly seen on Laputa in Castle in the Sky are also inspired by Nausicaa.
SD Gundam Force makes all sorts of references both obvious and subtle to past Gundam series. Lacroa's Knight Gundams are the main suits from Gundam Wing (and the princess is Relena), Ark's characters are all G Gundam characters, Neotopia and Dark Axis characters are from Universal Century, etc.
Especially notable is Professor Gerbera, who turns out to be a Gundam in disguise. From the future. The Gerbera Tetra from Gundam 0083 was originally designed in-universe as a Gundam, then modified and sold to Zeon when the Federation opted not to develop it.
Seitokai no Ichizon managed a brilliant one in the final episode via Shout-Out. Ken says he wants to establish his own erogeVisual Novel company, after which we pan to the logo of Key Visual Arts, along with him saying that it's based on the first kanji of his name. He then mentions two other companies, one of which is Leaf, the creator of the To Heart and To Heart 2 games, until we get the clincher to the entire Mythology Gag:
Ken: People who like my brand will be called Key-men. When something gets animated, the theme song will get referred to as the national anthem.
One episode had a duelist that looked virtually identical to Joey Wheeler with the same voice as him. The dub took a visual gag and made it much less subtle by naming him "Jesse Wheeler" and saying he was Joey's cousin — the original version didn't name the duelist and no mention of Joey was made.
Joey did mention having an annoying cousin that walks in every now and then.
And the same character, given the dub name Hobson, shows up in two, mutually exclusive scenes. In the manga, he runs Death-T2, in an arc that was never part of the anime. In the anime, he serves as the butler to the Kaiba family in a filler episode.
Towards the end of the Dark Signer arc in 5D's, Aki and Misty have their duel in a theme park named 'Monster World', which shares its name with the RPG that Yugi and his friends played with Ryou in the 6th and 7th volumes of the original manga.
Before the Ceremonial Battle starts, Yugi and the Pharaoh need to separate. The magic that does so first shows Yugi with two shadows, calling back to an iconic moment in the opening credits.
The plans for Siegfried's blueprints to his Duel Monsters holographic projectors resemble the Battle Boxes that were used in the manga version of the Duelist Kingdom arc.
The openings of Hidamari Sketch anime (at least x365's) make reference to scenes in the manga that never make it into the anime, such as Yuno's yonkoma-robot and camouflage Santa. Even they put in some frames that had just went to press at that time. See also Bait-and-Switch Credits.
A blink-and-you'll-miss-it example in Fullmetal Alchemist: The third opening for the new anime shows Fuhrer King Bradley aka Wrath right as the word "Pride" is sung in Gratuitous English. Take a guess who he was in the first anime.
More significantly, Episode 58 of Brotherhood features a cameo of an old woman who looks identical to Dante, Izumi's mentor in the first anime and also the main villain.
The outfit and briefcase Ed has at the end of the manga/second anime, when he's leaving and does his Wacky Marriage Proposal? Almost exactly the same as what he had in the Conqueror of Shamballa movie.
The Sacred Star of Milos's art style resembles the 2003 anime way more than it does the Brotherhood it shares a continuity with. Edward's facial structure is even back to it's more slender original series shape, and Winry looks like a mixture of the styles (2003 design but the full colored eyes of Brotherhood and the manga).
A more subtle nod would be the red shoes. In Noir, Kirika usually wears a pair of red/pink shoes. In Madlax (the second installment of the GWG trilogy), Vanessa buys a pair of red shoes for Margaret, which somehow triggers the latter's repressed memories, kicking off the main plot. In El Cazador, a pair of red shoes appears in a blink-and-you'll-miss-it camera shot inside Illis Gonzalez' home. Now, the real kicker is that all three of them (Kirika, Margaret, and Illis) are voiced by Houko Kuwashima, so there's no way it wasn't on purpose.
The 2006 Kujibiki Unbalance series references its past incarnation by bringing back old elements in new forms. The first Renko's tall and short Dumb Muscle reappear in the form of robots the new Renko creatres. The aliens from the first series' recap episode reappear as friendly aliens piloting a Mobile-Suit Human.
Franky from One Piece has a mythology gag as his catch phrase. He likes to say "I'm feeling especially super this week!" (though he often replaces 'super' with some other adjective.) New installments of One Piece come out once a week.
Also, the panel where Zoro decapitates a dragon is almost identical to the one where Ryuma did the same in One Piece Wanted.
The Death Notemovies have a couple of these, like Takada specifying Matsuda's death to be suicide by jumping off a building (in the original series, it was a ploy by L to fake Matsuda's death), and L using almost the exact same words Near used to counter Light'sMotive Rant.
There are two in the second arc of Pokémon Special. A Pikachu is babysitting a Caterpie and feeds it flowers when it gets hungry. Blue has a special microphone that can send messages in bubbles. Both are references to the Hey You, Pikachu! game. The FLRG arc starts off with a Nidorino and a Gengar fighting, just like the intro to the original games, Red and Blue (and their remakes). Later, Mewtwo gets trapped in a Restraining Bolt armor reminiscent of the one his anime counterpart wore when under Giovanni's control. Not quite sure if this counts, but Emerald's E-shooter is similar to that of the Pokémon Rangers' Capture Stylers. It's actually hinted in-universe that the E-shooter is based off of the Capture Stylers as well.
The first scene in the anime is actually the same intro from Red and Blue as well. The episode "Candid Camerupt!" had the characters watch movies, one of which features Isamu Akai from the gag manga Pocket Monsters.
Blue/Green's design from Special was also a gag of an unreleased female protagonist that was later revamped for the remakes as "Leaf".
Pokewake has a chapter with a young Giovanni, and how he met his Persian. He mainly just has a Persian in the anime. The last scene in that chapter also resembles Giovanni waiting for Red to battle him, from the Pokémon Red and Blue, downright to the shadowed boy resembling Red.
Recently in Naruto, the titular character's failed attempt to control his Superpowered Evil Side resulted in him turning into a small, shrimpy-looking fox version of himself, a reference to the series pilot where Naruto actually was a fox whose true form looked very similar.
In the first chapter, Mizuki tells Naruto that the secret everyone has been keeping from him is that he is the Nine-Tailed Fox. Mizuki's bending the truth here (that Naruto has the fox sealed within him), but it's also a reference to the pilot, in which after the Nine Tailed Fox attacked and was killed at the cost of eight of the chief's friends' lives, the chief (who resembles the Third Hokage, who resumed office after the Fourth's death sealing the fox) took in the baby Naruto out of pity. Interestingly enough, Mizuki's plan- to trick Naruto into stealing the scroll and killing him after he's done has some resemblance to the Big Bad of the pilot, who frames Naruto for theft and murder, and after he thinks his accomplice has killed Naruto, he gloats that people will think Naruto fled and is the real suspect.
During the beginning chapters of the first Haruhi Suzumiya novel, Haruhi makes it clear that she would like to meet an alien, esper, time traveler or slider. Turns out the series has at least one of each with the exception of the slider (it even has the ghosts, evil organizations and demons Kyon spoke of in the prologue). During the series the characters constantly wonder why they have yet to meet a slider, and even theorize at some point about Kyon being one (turns out he's not).
However, thanks to Yuki's retconning reality in Disappearance, Kyon can arguably be considered a slider though he's a perfectly normal high school student.
The ending of the Nakata arc in Amagami SS has the girl in question wearing a penguin suit with a smaller penguin attached to it. The scene could be considered this if you take into account her ending in the game, where she gets pregnant.
Wandering Son's art style is Watercolor-like. The manga's volume covers are almost always in water-color.
In the last episode of the anime, 19 minutes in we see a scene where Kaneda is greeted by a girl waving at him and a green haired boy. These two characters are from a manga released by Shimura Takako prior to Hourou Musuko, called Shikii No Juunin. The two characters have also noticeably aged since their appearances in the manga.
In the 2009 TV special of Kimba the White Lion, Kenichi sees a flock of birds that is very VERY similar to the one in the Japanese opening of the anime.