The last panel of thisBasic Instructions strip employs it when explaining superhero origin stories.
The Calvin and Hobbes incident is referred to in Freefall, with Sawtooth reminding Sam of the incident, saying "You know, the one you blamed on the spiky-haired boy with the stuffed tiger." Florence apparently gets to hear the details, but readers aren't privy to that particular piece of conversation. This is actually fitting, because on at least one occasion Calvin claims to have been framed by aliens for assorted mayhem.
Florence also found herself in such an incident in college: It involved herself, a forklift, and her go-to-sleep-instantly remote control.
There is even a Noodle incident with Noodle Implements, The royal family is not too happy with Sam due to an incident involving a zeppelin, a "Loop the loop" maneuver, and pudding. Lots and lots of pudding. This indirectly lead him to leave his home planet
The web cartoon The God and Devil Show had the Devil whisper the definition of "gomorrahmy" into Marilyn Manson's ear, playing on the common gag where one brings up Sodom and Gomorrah, mentions "sodomy", and then implies "gomorrahmy" was even worse. apparently it involved a petting zoo and toilet plungers.
Also, Zimmy's science fair entry. Antimony calls it an "abomination" and it is eventually taken away by men in hazmat suits despite Zimmy's insistence that it's not dangerous, but what she made was never explained.
And at the player level, whatever it is that Annie didn't want to talk about, after having dated Jim for a couple years between Episodes II and III.
Lampshaded by Jim when he mentions another Noodle Incident with Annie, occuring at an art museum.
Jim: I know we said we'd never mention it again, but I just wanted to mention it to show you I hadn't forgotten that we agreed not to mention it.
In the final confrontation between Obi-Wan and Anakin in Episode III, the comic manages to have a noddle accident actually happen within the story with Pete's cursed d20. However, since the comic always only shows whats happening in the game, we're only left to guess what's actually going on when they roll the die to see the outcome of Anakin trying to salto over Obi-Wan.
Also a Noodle Implement; by the description it's not really a die at all, and rolling it ended in fire.
Actually, that one's explained. You need to take the last word of the file names of every comic from November 12, 2002 onward, and they give you the text-only description of events from her lawyer's point of view.
Artie the gerbil gets turned into a human, and then realizes he can go in person to accept his Macarthur 'genius' grant. He says: "It won't be like that time we sent Mell to lecture at Caltech for me!"
Abner: ... I only had her rehearse her lines. There was no context. Agatha:(stunned) ... and when I asked him if that was a wrench in his pocket....
Also, while the members of Master Payne's circus plan their next performance:
Payne:...and then Dame Aedith will do her knife throwing act. Abner: And this time, do not ask if there are any vampires in the audience. Dame Aedith: Hey! How was I to know that guy was joking? Who'd joke about vampires!?
"While the Nuremburg Pudding Incident has been largely hushed up and reduced to tantalizing snippets of rumor and hearsay after the fact, the two things most sources agree on are that the Professoressa Foglio was probably mostly responsible (whether this was intentional or not), and that it smelled DELICIOUS."
It's been implied that Oggie did something that may or may not have caused Baron Wulfenback to keep a personal grudge towards him.
Sven's friend Wil leaves a pornographic piece of poetry in the coffee shop. Wil has the "brilliant" idea of getting Sven to go apologize for him, and the following conversation takes place.
Sven: What am I supposed to say? "I'm sorry that my friend is a creepy motherfucker, but will you please go on a date with him anyway?" Wil: Remember Elenore? Sven: Aw man, don't call in that favor now. Please. Wil: I'm calling it in.
Another one is used in a much earlier comic. Apparently, Pintsize has a large file in his hard drive of all the chaos he's caused. #472 is his favorite, because "Those preschoolers will remember that day for the rest of their lives." Knowing Pintsize, it's some kind of unholy wacky terror.
Jimbo has an interesting example of one where not even the participants know what happened: "All's I know is we went to a literary convention, I started drinkin', and next thing I know my agent's drivin' like a bat outta hell with me hid in the trunk and I ain't allowed in Canada ever again."
Alluded to in strip #410. If you hover over the comic, the Alt Text says "This is nothing. I once lost my genetics, rocketry, and stripping licenses in a single incident." How genetics, rocketry, and stripping can be combined at all boggles the mind.
And yet again in TED Talk. Though that one is so specific as to not leave much to the imagination ("The IAU ban came after the 'redefinition of "planet" to include the IAU president's mom' incident"). Most of the others were never explained.
Torg: Why did you jump to "Mark-5"? I don't remember Mark-3 and 4! Riff: I don't want to talk about it. Torg: And why are lots 189 through 205 closed for repair? Riff: I don't want to talk about it. Torg: And lot 206 looks like it's been partially liquefied! Riff:Drop it already!
Strip #488, a deva reviewing Roy's life mentions that Roy's grade school principal had quite a few choice things to say about him, leading Roy to exclaim, "It was just a joke! We didn't know Mrs. McNulty was allergic to weasels!"
A few comics later, the scene cuts in on a story (an apparently humorous one to boot) that Roy is telling the same archon.
Roy: —so I'm like, "But you told me we didn't want to turn right!" and Durkon says, "No, I told ye we dinnae want ta turn wights!" Man, we had to make a lot of Fortitude saves the next day.
Two on the same page: the MitD isn't allowed in Tsukiko's room because of 'that thing with the peanut butter.' And the crypt thing incident with Tsukiko (though this one is rather transparent, especially given her...inclinations).
The incident with the Rajah. Tarquin filled his mouth with creamed spinach and kept it that way for the duration of the coronation, as the punchline to some elaborate joke.
Just a little later, Vaarsuvius is shortly banished to the Semi-Elemental Plane of Ranch Dressing. When rescued some strips later, he is asked if he had any exciting adventures. Cue a Cut Away Gag about him saving Princess Gootrude from the sauce dragon for Prince Oozalot. Lampshaded as V responds he had no "exciting" adventures, to which Belkar breaks the fourth wall and replies that "Hey, maybe we will see that as a bonus story in one of the books." V then invokes this trope.
Every single Comments On A Postcard strip from mezzacotta is based on this principle.
A few involve Red Mage's book (in which he's writing, in D&D language, the things he's learning from the rest of the Light Warriors). The few pages we see begin with such things as "... my horse, I wouldn't have spent that year in college," and "that's when they made me their king."
These are references to other Noodle Incidents. "If it wasn't for my horse, I wouldn't have spent that year in college." is part of the Lewis Black's routine.
There is also this incident which occurs just off screen.
"...and that's when they made me their king." is said by Jack Sparrow in the Pirates of the Caribbean movie.
Black Mage also alludes to quite a few less-than-family-friendly events in the past during the comic strip:
Black Mage: Thief, your career as our leader reminds me of watching a blind child stumble through an uneven room filled with knives and tiger pits. Only not as interesting to watch because you can always push the kid if it looks like he'd make it. Who's mom's favourite now?! Red Mage: Wait. You murdered your own blind brother? Black Mage: It would have been cruel to let him live after what I did to his eyes.
Sinfest suggests a slightly risque explanation of the original Incident, here.
Sinfest has a Running Gag series of strips called You Had to be There, devoted to this trope.
The Hyena adoption ceremony in Digger consists of several complicated steps, one of which is described by Boneclaw Mother as "that stupid thing with the cactus spines."
What, exactly, the lyrics of "that one about the lady and the sausagemaker" are in Yet Another Fantasy Gamer Comic will likely remain forever a secret. All we know are the reasons it was written (to slander a woman the songwriter hit on and failed to score with) and that it takes about two years to clear the mental images out of one's head.
Future Dave (now Davesprite) gave John the code for the epic FEAR NO ANVIL, claiming he got it through "shenanigans".
"Shenanigans" is a general Dave-speak term for "the story is long and complicated to the point of comprising a whole novel on its own" with a dash of "I'm almost certain you would disapprove of my methods on either moral grounds, or the grounds that making your friends worry is generally considered a Bad Thing".
The Adventures of Dr. McNinja has never used Dr. McNinja's first name. Originally just a case of No Name Given, this is later handwaved in a conversation between Dr. McNinja and his clone (who goes by Old ... he has a farm, you see).
Dr. McNinja: Hey! You uh... You never told anybody our name, did you? Old: Oh, no way! Dr. McNinja: 'Cause, you know... the wizard. Old: Oh, I know.
Also, when a university-age Dr M. is talking to Benjamin Franklin about cloning:
In The Wotch, this rather hilarious exchange alludes to some past event that soured Kate to Jason. While the two discuss it in the actual comic, their words are covered up by the background events.
There's a couple of these in Schlock Mercenary, namely it's mentioned that Der Trihs used to be a tactical genius before part of his brain was eaten by a Borthwog torturer those whole story was actually a fabrication invented by the military to cover the fact they stuffed up a surgical operation they were performing on him, but it's never revealed what happened, or indeed who the Borthwog actually are.
Unicorn Jelly: two characters need to create a distraction, so they do the most shocking thing they can think of. The act is described by an un-translatable glyph. We never find out what it was, but later one of the characters says "Such a forbidden act, and it wasn't even all that interesting."
Kevin & Kell: The ex-human Danielle is asked if the family's human counterparts are also seen as unique within their world. She says yes, but doesn't explain why, saying there's no point dwelling on such silly differences:
"What could be more frowned on than a rabbit and a wolf?"
The end of a news report in a later strip: "... let's just say it was a Boston Baby Beauty Pageant nobody will forget any time soon! The gunman's identity has not yet been released by police."
Davan at one point opens up a spreadsheet of evil things he's done on purpose or accident. Most notably, this list inexplicably includes 'bake a pie' as well as an entry entitled 'Harness the power of kittens for evil'. This second one has happened 13 times.
A Game of Fools: Tomato's main gimmick (besides repeated crossing of the Moral Event Horizon) is telling horrible, traumatizing stories of his bizarre, awful deeds, the most of which we only ever hear the last few sentences of.
Tomato: ...so, I tried to explain that she DID give consent, but apparently that only applies when they're alive.
Once Sylvester gets a job as Tomato's... assistant, he gets in on the act too when telling work stories.
Chuck: I don't think we can. The supplies are usually on back order. 
Some or all of these "Noodle Incidents" could also be examples of Comic Sutra.
Platinum Grit. We'll never know what happened to Jeremy when he was carried away by Mexican strangers because it was "El Secreto del Corazon", a secret of the heart, and his silence was a matter of personal honour and great trust and faith. And because he'd been slamming mescal nonstop and didn't actually remember much of it.
Ichabod from Far Out There tells Kiki about a very strange incident, but we only hear a small part of it. The rest of us will probably never know where that epileptic pig came from.
Ichabod brings up another one later on. SHOULD he have known those Space Whales had "mommy issues"?
Monica of Wapsi Square once tried to use her dog to pick up guys in the park. It apparently resulted in her handbag catching fire.
Probably has something to do with her mother's own family background, which Diva knows about because she read her mother's diary.
The potato juice incident of 2005, Kitti and Dries's "legendary" anniversary, and everything Zac did on the Fleischmann account in What the Fu.
In an early Apple Valley, Doctor Hubris mentions that he is not allowed to enter Indiana ever again following the "Evil Corn" incident.
There are a couple in Our Little Adventure. The first being something that happened to Rocky and Angelika in Limbon River, and the second having to do with Angelika's first familiar. These incidents are not talked about, though many people make references to the familiar one in Norveg's company, which frustrates him to no end.
The "Project Noodle incident" in Weapon Brown. Which is (naturally) part of the origin story for that comic's version of Calvin and Hobbes.
Prequel has recurring references to a "pretty interesting party trick involving a yoyo and a pineapple" that is never explained - we are merely informed that it's not appropriate for most parties. Which still doesn't keep the main protagonist from performing it in the middle of the town square, although in her defense, she was completely plastered at the time.
According to a Deep Fried story, Beepo and Roadkill are bound together by a terrible secret that they can never tell anyone, and for which Roadkill can never, ever forgive Beepo. The only explanation we get is:
Beepo: Hey! That gross out contest was your idea!
The KA Mics referenced why Gertrude & Brunhilda had been banned from Tyrion here.
Karin-dou 4koma has a few references to a fight between various characters in the comic and an Evil Organization, during which—among other things—Shizuki fell in love with Tamaryu and Meguru got a major breast enhancement as a side effect of being aged down and back. This comes from an H-doujin the author privately circulated among friends but never released.
Precocious: Whatever the Sapphire kids did preceding their hiding out at Kaitlyn's birthday party. One by one, supporting characters learned the details in tiny whispers indecipherable by the audience.
Almost all of the children's unseen escapades are treated as Noodle Incidents unless the joke or plot specifically requires otherwise, as well as wealth of Noodle Implements in play when their schemes have yet to come to fruition.
Subverted with Tiffany's aging. Strip 893 presents the accident that halted Tiff's aging as a Noodle Incident, but strip 896 provides an explanation.
The "Orlando Incident" let the adults in on the fun.
Heck, there are so many Noodle Incidents in the comic that it's even addressed in the FAQ!
Question: Will we get to see what happened when _____?
Answer: Probably not. I think some things are funnier when you have to imagine what crazy stuff went down yourself!
Given that the author admits to taking a lot of inspiration from Calvin and Hobbes, the frequency of this trope's appearance is not really a surprise.