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.
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 favorite 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.
The comic 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.
Chapter 29 gives us the full story: Doc's grandfather sealed away a ghost wizard that was about to kill Young Doc (because Young Doc was kind ofan idiot). He used Doc's name and his own life force to cast the spell. Doc is the only person who remembers his name and if he ever says it, the seal will be broken.
Also, when a university-age Dr M. is talking to Benjamin Franklin about cloning:
Mitzi: Who would call us on Katakana? Your dad's still dead, right? Dan: Well, we'll never really know for sure, but I doubt he'd just call.
The Adventures of Sue and Kathryn! implies part of the reason everyone is so afraid of Sue is because of the block party massacre last year. All we know about that is that Sue claims she was "totes provoked".
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. We do learn what it was much later; Annie was working as a waitress and didn't tell Jim, Jim took her out to the same restaurant not knowing this, he made a scene, and she got fired. She realized after saying it out loud that a) the firing was unrelated since she was terrible at her job, and b) she was being completely unreasonable.
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 noodle accident actually happen within the story with Pete's cursed d20. However, since the comic always only shows what's 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.
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 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".
Corlis: Well Moppy thinks it's a Kaar'Latch, a giant psychic five-eyed exoskeleton clad creature that is said to feast on the souls of young dragons.
Lemuel: Yeah, but Moppy thinks everything wants to feed on young dragon souls these days.
Corlis: Well, he was right about your sandwich wasn't he?
Dresden Codak: "Remember when Reverse Moses parted the city to escape Aqua-Pharaoh?"
Much later, Kimiko states that she's never been convicted of a felony in the state Nephilopolis is in, and insists that she gave the bones back. Then she gets distracted before explaining exactly what that means.
At some point prior to the start of the story in Drowtales, Laele'aell Val'Sarghress was (apparently) possessed by a demon and an attempted exorcism resulted in her becoming an Empty Shell, which created a situation where the Sarghress clan had no heir apparent and made her mother Quain'tana resort to desperate measures. There was going to be a story at one point clarifying what exactly happened but it was never made for unknown reasons.
In the webcomic Earthsong, Zaebos threatens to tell of Felucca's role in a literal Noodle Incident.
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"?
In The Fourth, we know that Skärva's great-grandfather and the first's partner did something to bring the curse upon Skärva's line, but every time WHAT they did otherwise naturally comes up in exposition, the speaker talks around it.
The Calvin and Hobbes incident is referred to, 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, a graduation ceremony, 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
When Florence is woken up in her pajamas, tied to a chair, with two angry humans and a robot standing over her, she mentally notes that it's the fourth worst awakening she's ever had.
"If I tie your facial tentacles to the overhead rack, it will take you three minutes and forty seven seconds to get loose." "That is something I wish you didn't know from experience."
Ultimately, Sam might as well be made of these. This time, it's the reason why he's running from a mob of police officers. (It's not all bad. Being a one-squid crime spree, he almost single-tentacledly keeps them in business.)
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.
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....
The other Heterodyne plays and stories are just as bad. Why does Race to the West Pole end with Klaus in a barrel?
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.
Ognian:"Shoddop 'bout dot!"
"And that was the last time Professor Phosphorous visited the fireworks factory. Or anything else, really."
The entire concept of the Island of the Monkey Girls was one for a long time. It was eventually confirmed to be a night club in Paris... but when a fan asked what Zola thought Gil could have done to get himself imprisoned in the Castle, where the Empire sends people it wants to disappear, the only explanation supplied was "Zola was Head Waitress at the Island of the Monkey Girls Theatre and Showbar in Paris." So that's still an enigma.
We get a interesting one while the group is in the the hidden library. Even Agatha remarks that she has "much to learn about the rich and varied history of Jägers".
Agatha: Maybe it's a Jäger Shredding Machine! Dimo: No vay. Dey melted dot down.
The story of Baron Wulfenbach's exile. He suddenly disappeared before Lucrezia and Bill got married and came back with an infant son a few years later after Bill, Lucrezia and the Other are gone. Finding everything is in chaos, he resolved to impose order by amassing forces and built his The Empire. What happened between he disappeared and he got back is ripe source for gossips. (Though in real life, thanks to a sketch drawn by Mr. Foglio, fans at least know where he was sent: Skifander.
The novelizations are full of vague references to bizarre things done by various Sparks.
Downplayed in a side-story comic with regard to the extra deadly sins invented by the Heterodynes: "Gomorrity" is apparently not all that unusual, but we still don't get to know exactly what it is.
Girls Next Door makes use of this trope, with a never-elaborated upon Prom Night Incident.
There is also the Sushi incident which barred Erik from the cast's favorite sushi bar.
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.
A rare almost-on-screen example in Godslave - we don't know just what trap Anpu sets up for Turner and Blacksmith's curses and electric flashes are the only clues.
Tedd: In retrospect, that griffin was probably noteworthy. Elliot:She was just asking for directions!
Sydney, the main character of Grrl Power was once arrested for aggravated assault (although it was dismissed as self-defense). However, it is a little unclear what she actually did. While we do see a possibility in the form of an Imagine Spot by Maxima, the actual police report merely reads, "Oh the humanity!"
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.
In Head Trip Mal has a party that involves alcohol and Disney movies and when she comes to she finds she's taken over Disneyworld with superpowers granted by costumes and Disney movies. Aurora costume gives sleeping powers, Belle costume can turn anyone into furniture but they decided using the magic mirror for surveillance was more practical, Megara has Hade's power as a loophole states any power from the movie is granted by the costume, Snow white has the ability to summon animals to do her bidding. However when they get to Alice they have no idea what her power is as she showed Mal when Mal was under the influence of "The Shot" and Mal made her sign a contract to never use or speak about her power again. All the other ladies know is "it involved hearts" Considering how Mal has repeatedly been wooed by the Devil himself because of how horrible she is one can only wonder what power would be forbidden.
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 (Jade uses it later, as well) 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 that making your friends worry is generally considered a Bad Thing". Karkat considers it "INFURIATINGLY VAGUE" (Warning: spoilers).
GC: PL34S3 K4RK4T, DO NOT PR3T3ND TH4T YOU FORGOT 4BOUT OUR L1TTL3 MOM3NT
CG: YOU MEAN
Due to the Anachronic Order of the series, a lot of incidents that start out as examples of this end up explained later on. For example, the FLARP accident that crippled Tavros and blinded Terezi.
Jack Noir's Jailbreak Adventure gave us the line "You've never once been disappointed to receive a pumpkin full of knives, and you're not about to make an exception."
The final battle between the Trolls and the Black King of their session is mentioned a few times, but never actually depicted beyond one or two still frames, which establish two things: 1. the Black King was utterly enormous and 2. Aradia and Sollux used their telekinesis to throw meteors at him at some point. The noodliest part of the fight, however, is Gamzee's contribution: at some point he snapped and did... something to the Black King that caused more damage in a single hit than anything else the Trolls did (including Vriska, who was the only one among them who achieved God Tier). Whatever happened, it terrified the crap out of the Trolls, and none of them seem able to explain just what exactly Gamzee did, or more importantly, what it was that set him off.
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.
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?"
In oneMegamanspritecomic strip, Zero shows Megaman his new disc player, which can play anything. Megaman suggests a shrimp disc, but in the next comic it has Megaman and Zero agreeing to never do that again.
MegaTokyo: Piro and Largo's roadtrip to Canada: "Hey come on... we got handcuffed by real Mounties! That was cool."
Every single Comments On A Postcard strip from mezzacotta is based on this principle.
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!"
Yeager in Nodwick invented an eighth deadly sin. All we know about it is that Yeager found it entertaining and called it "blasphotrociterra-o-rama".
In another strip he is confronted by four people he bullied as a child. Two of the incidents are pretty self explanatory but one is only described as ruining a girl's first date with a "fish catapult" and another is considered so heinous it is only referred to as "the cheese incident".
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. All we know about it is that Tarquin spent the entire coronation with his mouth full of creamed spinach, as the punchline to some elaborate joke.
Nale refers to something happening when he was five that drove him to spend twenty-odd years planning to murder Malack. Given Nale's animus at the time it seems likely it either involved damaged pride, childhood trauma, or a mix of the two.
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.
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.
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.
Ozy and Millie had a different one of these for each joke that calls for one.
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.
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!
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.
Another one is used in a this 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.
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.
And, of course, with the reappearance of Steve we have only vague hints into what secret agent-ish things he was doing while he was gone.
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."
Realtor: By the way, you're not a witch or wizard or anything, right? Dora: Uh... no? Why do you ask? Realtor: We had to institute a strict no-sorcery policy because of our last tenant. Dora: What? Why? Realtor: Let me show you the kitchen.
Claire: Why do you have a detachable butt? Melon: Why wouldn't I? Claire: Fair enough. How did you lose it? Melon: I didn't MISPLACE it, so much as it was DESTROYED. Claire: O-oh. What happened? Arthur: Actually, I did some calculations and it could theoretically be in low earth orbit.
Randomly Assembled: Birthdayboy's arm injury was *not* a result of the infamous "noodle inceedeent* (which, apparently, everyone has heard of), it happened much earlier, when he was apparently hit by a motorcycle.
Apparently some time before the events of The Sanity Circus, Bee the circus clown was involved in a magic accident that left her with Raymanian Limbs. She's surprisingly ok with it.
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.
In Seiyuu CRUSH!, we learn at the beginning that the CRUSH! agency was the only agency willing to hire Kaji "after what happened", but it isn't revealed what actually happened.
A few in Sharp Zero, mostly involving Elliot. There's the story about him getting banned from two IHO Ps (a goat was involved in one),and when Elliot comes in contact with the titular toxic chemical substance he says, "Somehow this isn't as bad as the Ikea incident."
Sinfest suggests a slightly risqué explanation of the original Incident, here.
Sinfest has a Running Gag series of strips called You Had to be There, devoted to this trope.
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!
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.
The Västerström is several times mentioned to have undergone a Riches to Rags episode some years earlier due to its relevance to their current situation, but the cause has yet to be mentioned three real-life years and thirteen chapters into the story.
The piece of Blackmail that Trond used to convince the captain a merchant ship to make a detour into the Silent World to deliver food to the crew. All that gets shown is the reaction of the captain as Trond reminds her of the information.
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 untranslatable 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."
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.
This What-If strip is composed mainly of various horrifying Noodle Incidents.
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.