In the sprite comic Bob and George, the fourth wall never existed, and it was a constant running gag. All the characters knew that they were in a comic, and the author of the comic often made appearances. Once he even came out to fight another author that entered his comic's universe. One of the characters even read ahead to know what was going to happen next. Of course this wasn't exactly a bad thing, as it made the comic what it was.
In PvP, now and then, the characters break the fourth wall, usually for some movie impersonation. Nearly every time, someone dies horribly, but as it's fourth wall breaking, it gives an excuse for a Snap Back.
Scandinavia and the World occasionally breaks this, but without referencing it. Whenever the Netherlands and Denmark, (and sometimes Germany) surprise Japan by making out, they call it Yaoi, with is never real people; meaning that they, even if it wasn't intentional, know that they know that they are drawn.
The first entry of The Rifters has Tobi addressing the reader, telling them the title of the comic they're reading.
In Acorn Grove, after a long break, the creators of the strip write themselves in to apologize for the last strip being there for so long. . In another strip the resident redshirt get killed when he notices the fourth wall .
"Dr. McNinja's Final Thoughts" breaks the fourth wall at the end of each chapter in The Adventures of Dr. McNinja (usually used to deliver a humorous 'lesson' from the story or a moral of questionable veracity)
The Insecticomics wavers between breaking the fourth wall and not having one altogether. The Insecticons themselves don't really seem to bother with it.
Done (incredibly skillfully) every now and then in Dragon Tails.
Corlis: That's it, I'm finding a new comic, this one's stupid!
Rich Burlew's The Order of the Stick is pretty random with the fourth wall. The worst is probably the Oracle constantly addressing the audience and referring to books or in-comic years. Also the 100th and 600th strip had lampshading referring to the anticlimax in each. And V once referred to how many strips would be necessary to get another dumb trial done. Belkar also once referred to himself as the only funny thing left in the comic strip.
Strip #649 memorably includes Haley stealing a diamond from the site's cast page (which is not part of the comic's continuity) in order to power a Ressurection spell. Ever since then, the actual cast page has shown Haley holding an "I owe me" note instead of the actual diamond.
One of the prequel books shatters the fourth wall in a brilliant way.
Elan: Good evening, innkeeper! I require a room [...]
Innkeeper: Of course, sir. What kind of room did you have in mind?
Elan: Well, I was thinking of something with a ceiling, a floor, and four walls.
Innkeeper: Are you certain, sir? Because rooms without fourth walls are very popular in this comic strip.
Beat Panel while both smile and wink at the reader.
In Keychain of Creation, a comic based on the Exalted tabletop RPG, the characters frequently talk as if the rules of the game were the solid rules of their reality, and they knew their own stats. However, they don't actively break the fourth wall; that's left to a band of the Fae, especially their leader, who says quite frankly that he only led his band back to fight the main characters because there'd be no story otherwise. The main characters all act like he's a jabbering mental patient when he says as much.
Shape Quest, an RPG video game parody comic, does this during the first strip, where Lance acknowledges that he is poorly drawn and tries to think of something clever to say so people will continue reading past the first strip.
In Drowtales, Kiel can tell that the readers are there and talks to them when she's bored. Others consider her weird for still having an imaginary friend.
In a rare twist of breaking the fourth wall in a tragic rather than comedic manner, Kiel grows furious at the audience watching her and throws a belt at them. According the forum fandom, it broke many screens and hit many eyes.
Darths & Droids' 468th strip says "Puny Comic-Reading Humans, Bow Before My Magnificence!".
In an early Faulty Logic page, Fox and Jalyss break through the fourth wall of the author-comments section (with a hammer) to make sure there are actually people reading their strip.
More recently, a spacial vortex reverses fourth-wall positions. Notably, readers can actually see the Fourth Wall in the background.
The xkcd blag features "Federal Reserve Skateboard: A Short Story," which includes the following:
Bernanke, trying not to slip in the patches of blood on the floor, struggled with Greenspan. The older man moved like a snake that moved like a former Fed Chairman who moved like a ninja. At last, Bernanke got a solid grip on Greenspan?s collar and hurled him through the fourth wall, knocking you to the ground.
Penny from Out at Home pretty much exists to break the fourth wall, to the confusion of the other characters, who don't have her Medium Awareness.
"Why are you talking to that wall?"
The Cyantian Chronicles: Mostly averted in the canon comics. Only NOT averted when "We Have a Shivae-13 Rating To Maintain", which only happened once so far.
Played for laughs in a fan scripted bonus comic contained in the print version of Akaelae 5.
In the hundredth strip of Loserz, protagonist Ben remarks: "I just got the strangest feeling, like I'm being watched. — What's even weirder is that I'm somehow sure this has happened exactly 100 times..."
Too Much Information has a solid Fourth Wall, with one exception. There's an auxiliary webcomic called Maddie's Monster, in which one of the regular characters (Maddie Cartman) meets an Eldritch Abomination named G'Nar The Insignificant. G'Nar, being non-human, can see through the fourth wall, and tries to point it out. Maddie is unable to figure out what the heck he's talking about.
Flying Man and Friends does this on a regular basis, with characters addressing or reacting to readers. In this strip, there was even an actual wall underneath the comic, which was peeled away to reveal it.
Nowhere University has the characters make references to plot twists & their author, then again the teachers at that school come from literary classics so...
In the "Little Diddle" comic Lucky Day◊ little diddle finds a lucky penny and lucky ducky says there is no such thing as luck. little diddle then says that they are in a comic so it does exist, then lucky says that the fourth wall just broke.
Untitled! had elements of this early on, with, for example, a character who was introduced as "living in the gaps between frames," complete with a character grabbing the frame and leaning her upper body out of the frame and looking into the afore-mentioned gap. What makes this case interesting is that the comic later caught a bad case of Cerebus Syndrome, and as a symptom, acquired a fourth wall. Some of the fourth-wall-breaking elements where explained away (e.g. as the actions of Sufficiently Advanced Aliens or psychic planeswalkers): I don't recall an explanation ever being provided for what was happening when the protagonist leaned her upper torso out of the frame.
ThisSMBC comic has the entire human race break the fourth wall of the universe after figuring out that it is just a simulation.
In Homestuck, there is an actual goddamn physical fourth wall. It's first used as a lame joke and then later by the author as a self-indulgent insert to the comic where he recaps the story. Then the comic introduces a fifth wall (according to Word of Hussie, it separates multiple omniscient narrators) and promptly starts breaking that, too. It's strongly implied that this will be a major plot point. On his formspring page, Andrew Hussie joked that there's also a sixth wall, and that it's what's holding back all the "shitty memes". That wall apparently broke a long time ago.
Every chapter of Tales of Gnosis College ends with a "Women of Gnosis" pin-up that depicts one of the series's female characters and contains a brief caption. One of these characters — Iris Brockman — uses her caption to complain to the reader about how she got neither a name nor a dialog line in the preceding chapter.
Rarely done in Arthur, King of Time and Space ... at least within the panels (there are frequent No Fourth Wall strips with the characters against the plain background of the website, meant to be "backstage"). However, the court of Carbonek starts doing it during the "Lancelot is found by King Pelles's men and recovers from his wild man phase" storyline. Lancelot eventually calls them on it.
Grrl Power seldom does this, but the splash page for chapter 2 does it quite deliberately. Sydney sees the ARC building for the first time, and looks up at it, with the 'camera' behind her and panning upward:
Sydney: ...I thought you said ARCswat. Maxima: I'll explain it on the next page. Sydney: ...there had better not be anyone photographing my butt.
End Of Infinity: The author breaks the fourth wall to tell the characters that THE POWER OF TELEGRAM COMPELS YOU. The Telegrams are direct commands from the readers to the characters.