The Child of Love: In chapter seventh's omake, Asuka berates the author because he is lazy and hasn't updated his website.
Superwomen of Eva 2: Lone Heir of Krypton: The characters frequently break the fourth wall in the omakes: the author and Asuka talk about his discarded ideas, Asuka complains of a thug breaking the fourth wall when he accused her of doing blatant shout-outs, Shinji gets a present of the author, or the author decides to address the characters.
Pinkie Pie breaking the fourth wall to acknowledge or even directly address the readers and/or the author is something of a Running Gag in FiM fanfiction in general. Sometimes other characters get in on the act, more often it's waved off as her just being Pinkie.
In The Last Airbender parody Bring Me All Your Elderly, the Animated!Characters not only are aware that they are animated (and discuss it very casually), they also leave the Animated!Universe to enter the Movie!Universe, generally blame all unexplained events either on the fanfic author or M. Night Shyamalan, read their own fanfic and comments straight off the internet, and basically suffer severe existential crises as a result. The fourth wall itself actually makes a brief appearance at one point in the story, along with a sign that says "fragile."
Mai: But for future reference, guys - try to be careful about breaking the fourth wall around Zuko, okay? He doesn't know, and it tends to freak him out a little.
Zuko: Fourth wall? What wall? Someone broke a wall?
Sweetie's Mansion: Pinkie Pie still has this ability even as a brainwashed ghost that is out to kill Sweetie Belle. Upon catching her, Sweetie gains this ability as well and unintentionally calls the author out for the direction the story is going when she's in Lotus-Eater Machine.
Pinkie Pie/Discord: It’s canon to the comics, don’t worry about it.
At the end of Paper Mario X 2: The Thousand Year Door, Link puts out a velvet box out of his bag. Inside includes a ring which he uses to propose to Zelda. The very last line is Link addressing to the audience: "Can you guess what I'm going to do?"
Imperfect Metamorphosis: In a rare totally serious example, Yukari inadvertently weaponizes this against Yuuka when she reaches into her soul and generally rips things apart. This leads to Yuuka periodically taking over the narration and speaking directly to the reader, as well as adjusting her myriad plans to manipulate the established narrative.
The first hint towards this comes in a memorable Madness Mantra ("It can't be. Just words on a page. It's all paper. And not even real paper.") which Yuuka keeps muttering to herself while ignoring being pummelled into the dust by Yukari.
The Reading Rainbowverse has as its central concept the idea that various ponies are commenting on comics and answering questions. That's not this trope. What is this trope is when a reader pointed out to Gilda her blog had been hijacked by a mysterious "mod" person, resulting in the two having a bit of a tussle.
A New Order: Helios does this when speaking with the ghost of Queen Serenity. He and she both know the secret of the Time Gates (him because he read her mind) but he asks her to explain it anyway because the people on the fourth wall don't know.
In the Medaka Box fanfic World As Myth, Misogi Kumagawa recognizes when bold font and italics are used in dialogue.
Anshin'in seems to be aware of the events of the original manga.
In Amber Night and the Curse of the Diabolical Pastry Thief, a My Little Pony: Friendship Is Magic fanfic, Amber Night is apparently no stranger to the "sadistic hairless chimpanzee pounding away it the keyboard that controls the fate of the pastryless pony" on the other side of the fourth wall, demonstrated in the beginning when she grows inspired by his monologue without having heard it, and again later on when she convinces him to disable the gym's laser defense systems.
Super Smash Bros fanfiction Ten Random Characters suffers varied degrees of abuse from the characters, and often, the author. It is broken so frequently that the wall is given a codename, the Norfair Alley. Sometimes, this trope is quite literal. Taken Up to Eleven in Chapter 11, in which a mob of fangirls invades after the fourth wall quite literally falls down dead.
Ginny: (thinking) I can't believe that was only yesterday. It seems like one day lasted several chapters for no particular reason.
The original Dante's Night at Freddy's was no slouch when it came to Leaning on the Fourth Wall, but its sequel, Animatronic Boogaloo went so insane that, around chapter 8 and especially in chapter 9, the author describes the events as, "Dante and MJTR destroy the fourth wall, take it around back, and beat it with its own body."
In New Reality, Mithos jumps into the real world to kidnap the heroine, making it an In-Universe example.
Jessie: What could we even use this thing as, a cannon? James: None of this is canon, Jessie.
In the MST treatment of Tom Swift and His War Tank, Joel and the bots become so frustrated at Ned's stupidity that they run out of ways to riff him and are forced to ask the readers for help.
Fan game Rakenzarn Tales has two primary offenders: Axel Akamura, an OC who's implied to be from outside of Rakenzarn like Kyuu, and Deadpool himself, who even does his own special skill descriptions.
Much like the cartoon on which they're based, Cinderjuice and its sequels take any number of shots at the fourth wall. One reviewer asked whether the fourth wall had killed the author's father, since it gets shattered with so much frequency.
In the House fanfic "Iggy Pop Go The Zombies" a literal piece of wall collapses when another character tells House, "Quit making that face, you look like Bertie Wooster."
Stage 7, the Kamen Rider Drive tribute chapter shows Shinnosuke's shocking expression when Samus wakes up in the Drive Pit as he and the others attempt to forcibly dissect her Fusion Suit, he says while bringing up his series' main writer, "Is it just me or was the writer fond of police dramas?!"
Stage 17, where Samus, Takatora, Mitsuzane, and Go confront a resurrected Kaito Kumon, after they transformed, the song "Supernova" from Kamen Rider Kiva plays, leading Go to tell the writer the music is inappropriate, much to Takatora's annoyance.
Go: HEEEYYY! This is NOT Kamen Rider Kiva! Why bother play that damn music?!
Takatora: Jesus Christ! Eyes on the battlefield, Shijima-kun! Who are you talking to, anyway?