The second OVA for season 3 is a never ending string of jokes at Studio Shaft poking fun at themselves and their own series. Such as thanking viewers who "came across the opening and didn't change the channel".
Nobuhiro Watsuki has done this every time he has some free space in his character dossiers note Usually along the lines of, "I meant for this character to look like John Travolta, but it didn't turn out so well. Sorry for not being talented enough." or his "Free Space" sections, particularly in his series Rurouni Kenshin. At one point he had Kaoru remark that Kenshin's handwriting was "as bad as Watsuki's."
Mitsuru Adachi does this a lot. His characters make fun of him for the lack of variety in his drawings, often respond with "who?" when he gets brought up, and most of the time when he draws himself into the background he's being chased by angry editors. Also, the cast members in H2 go to an Adachi art show at one point. They all agree that it's terrible.
The first episode of Excel♥Saga has Il Palazzo assigning Excel to start killing off all manga-ka, starting with their own creator, Koshi Rikdo. The pastiche of a self-insert that she encounters is Too Dumb to Live, anyway.
Plus, he's singing a little song to himself about how manga-ka are degenerate scum who are as fleas to the people of Earth.
Hidekaz Himaruya, the author of Axis Powers Hetalia, once jokes both about himself and his fans concerning his chicken-scratch (that gives scanlators a very difficult time).
Author's note: If you can read my handwriting, you have too much free time.
Quoth France in the Gag Dub upon seeing America's drawings of them; "Those drawings are even worse than our actual animation!"
The (American-produced) English dub also seems to take a few potshots at Americans that weren't in the original show:
Narrator: ...and to translate all that for American viewers: a bunch of stuff happened in other countries that didn't involve explosions and kicking ass.
Italy may be the useless ditz, but he's well-aware of it and eager to point it out.
Italy (to Germany):"You can order me around and I'll disappoint you!"
Italy (to Japan, showing him a haunted place in his home):"But you don't have to worry about [the ghosts]. They are Italians, after all!"
Used in Seitokai no Ichizon. In the first scene, when the cast are discussing how to adapt their own series to an anime (it's that kind of show), Mafuyu reads a negative review of their own light novel from Amazon.
At another point, Ken says that he likes the harem ending because "everyone is happy." The rest of the council calls that a stupid idea. Ken checks a copy of the series' first light novel, stating that in there they said he was alright. The girls call their idea in their own source material stupid.
The creator of One Piece gives himself one in a movie short. In it, he's called as a ringer to make the deciding point in a soccer match. He kicks the ball and...it's easily caught by Coby (who at the time was one of the weakest characters in the series). Not only that but he announces his failure in the commentator box before he is promptly beaten up by his team members, all of them bad guys from previous arcs who had already been defeated by Luffy.
Or in One Piece proper, during Luffy's fight with Arlong, when Arlong questions what Luffy can do as he flails at him with swords, he responds that his friends will save him before punching him in the mouth and breaking his teeth. His listing of the things he cannot do, while showing the crewmates who can do those things, overlaps with Badass Boast
Luffy: I don't know how to use a sword, shark face!!!
Yosaku: What's he on about?
Luffy: I don't know how to navigate either! I can't cook! And I can't tell lies!
Luffy: I know I can't live without help from a lot of people!
In Bakuman。, The Time of Greenery, a manga created by Aoki, is based on the main characters' romance, in which they decide to marry once they achieve their dreams, but not even meet until then. Eventually, it gets cancelled, and Yoshida suggests that the story has been stuck for a while, which could be a reference for Mashiro and Azuki's promise taking a long time to fulfll. 10 in-universe years, to be exact, and they're little more than halfway there as of Time of Greenery's cancellation.
While there are lots of Take Thats aimed at the dub version of Yu-Gi-Oh!, the dub actually did it to themselves during the Crashtown arc of Yu Gi Oh5ds, it appears. In the first part, Yusei dueled three men, and rather than use the catchphrase he usually uses in the dub, he used Judai Yukai's catchphrase ("Get your game on") from the previous series in the franchise, a very common target of a Take That from fans. Or, possibly, it may have been intended to lighten the Darker and Edgier nature of the arc, (considered unusually dark even for that series, which was itself rather dark when compared to the others in the franchise.)
Actually, that's not the first time the franchise did something like that. There was this exchange between Amon and Majyome during their duel in Season Three of Yu-Gi-Oh! GX.
Amon: I activate my Trap Cards!
Majyome: How can you do that?
Amon(Sarcastically): I call out their names dramatically and they lift up, how long have you been playing this game?
And before that there was this exchange between Pegasus and Napolean in Season Two (keep in mind that Pegasus did always have a weird sense of humor in both versions):
Pegasus: But only on the condition that you both can defeat me.
Napolean: You mean in a duel?
Pegasus: Well I certainly don't mean a bake-off!
And yet another, courtesy of the dub:
Chaz Princeton: Who CARES if he's richer than me, and more powerful? I'm really good at playing card games, and isn't that what life is about?
And who could forget this one? Seems the show wanted to make light of how annoying fans found the Catch Phases:
The Fanservice of Fairy Tail has increased a lot throughout the years, to the point that there sometimes seems to be a nude scene every second chapter. In chapter 355, when the girls are skinny-dipping in a hot spring, they discover that the guys are in there with them. Of course, Lucy and Wendy freak out about being seen naked, but Natsu calmly replies that "we've already seen you naked a lot of times", and Gray adds "yeah, the novelty of it has worn off". Since this line was exactly what many readers were thinking at the point, and the fact that Natsu and Gray actually only have seen Lucy naked a couple of times in-universe, it is widely thought that the author used the two guys as a way of admitting that the fanservice had possibly gotten a little too over-the-top.
Episode 23 of Happiness Charge Pretty Cure has Hime and Iona going grocery shopping as a way to bond. As they do, Hime ends up finding a bag of snacks proudly boasting some of the International Cures and even coming with a special card inside. Iona's incredulous over it and wonders why Hime wants to spend money on that junk.