A.A. Pessimal's short story the Pinky-Swear expands on a Suspiciously Specific Denial made by Bernadette in-canon. The story refers to an outbreak of a certain epidemic in Africa and wonders out loud if Bernadette's famously relaxed attitude to lab discipline (with Amy's inadvertent connivance) might have somehow contributed. And the pressing need for a pinky-swear binding all parties, never to speak of this incident ever again, so long as we both shall live, amen.
Last Child of Krypton: In chapter 6 of the Redux Asuka runs into Shinji at the arcade and he leaves shortly after. Later he is not in home and she goes back to the arcade and starts looking everywhere. Pointedly and out of nowhere she thinks: "There was one thing she wasn't doing at all, which was looking for Shinji."
Hanyuu in Kyon Big Damn Hero follows Kyon when he's bathing only because she's worried about him. She has no ulterior motive to keep an eye on him, or admire his surprisingly toned physique as he patiently watches over one of his younger cousins. She's just ensuring he was okay, unhurt after the mysterious events, and that's the only reason she's staring at him so closely!
Kanae didn't slide into Kyon's bed intentionally, nor did she do anything with him while sleeping there. Subverted, because Haruhi believes her (as Kanae was telling the truth) though she can't help but to lampshade it.
When Team Mario meets up with Team Luigi in chapter 64 of Paper Mario X 2, Luigi finishes his backstory with "…and so we stopped here for a rest after NOT seeing Bowser, Eggman, and Ganondorf randomly head to the east area!"
In chapter 7's omake Shinji catches Asuka playing with dolls:
Asuka:"What did you see?!" Shinji:"Nothing! [...] I didn't see you playing with your dolls!"
In chapter 11 Asuka thinks it is disgusting as Misato is taking advantage of Shinji's caring nature to get him taking care of her. She is angry because it and definitely not because Shinji is paying a lot of attention to Misato:
Not that he minds, Asuka thought dourly. Honestly, the boy took to the task of playing nursemaid with far more gusto than she felt a man should. It was almost sickening how Misato was taking advantage of Shinji's caring nature while she was ill. Asuka wasn't the least bit jealous of attention he had been lavishing on Misato. Really.
Turnabout Storm: Apple Bloom claims in her testimony that she heard a lightning bolt while in the forest, and says that it definitely didn't scare her. Phoenix catches wind of this and presses further, revealing more information in the process.
Much later, after the trial is over, Trixie is invited to one of Pinkie Pie's impromptu parties. She adamantly declares several times that she does not want to attend, stating that she's only doing so as a punishment. Her expression at several points gives lie to her words, however.
In Unfamiliar, Siesta does this with regards to not speaking ill about Count Mott. It's also inverted, however, when Kirche notes a lack of denial about Alex being a plaguebearer.
In Legacy Flynn is very specific that he's not an "axe" murderer. Hatchets? Hidden blades and other tools? that's a different story
Blue Beetle: When there's really nothing wrong you always say stuff like "There's always something wrong in Gotham!" or "Is anything ever right in this world?" Am I right?
Batman: ... I hate you...
Teen Titans The Abridged Series: Starfire says she uses happy thoughts to fly. Raven asks what she thinks of and Starfire says she thinks of Robin. Raven asks if she means her friendship with Robin. Starfire says that's it, and nothing else, and certainly nothing involving chains and hot wax.
Light: Of course, I kept up the appearance of being the perfect specimen. I was smart, personable, and damn sexy. Oh no, there's no narcissistic complex here—it's just another statement of facts; my genetics were damn good.
Also Light becomes obsessed about winning in the seductive game he's playing with L even though he frequently claims that L disgusts him.
In a fanfic series expanding Sir Terry Pratchett's Discworld series, author A.A. Pessimal would like to formally deny that the country of Rimwards Howondaland has anything at all to do with the Republic of South Africa in the old apartheid days. Even if apartheid is such a crazy concept it might as well have originated on TP's mirror-world. (Discworld apartheid is currently being tested by immigrant Igors, who have a terrible habit of attaching body parts originating with black people onto whites who need an upgrade. The Rimwards Howandalandian Staadt is still trying to racially classify the results of Igor interventions.)
Nor does the Vondalaans language have anything other than superficial similarities to Afrikaans. It is simply the original language of Sto Kerrig, a Discworld nation justly famed for tulips, clogs, windmills and that cheese with the red outer rind note that nobody ever tells you not to eat, transplanted to Howondaland, with white settlers from SK. Right?
And Sto Kerrig is not Holland either, despite the tulips, and the unmistakeable fact that neighbouring Sto Lat is, like Luxembourg, a Grand Duchy, while Sto Helit (like Belgium) grows lots of sprouts and cabbages. Now go to The Black Sheep, and read on...
Hawke: Don't I remember hearing that you once killed three kids? I don't think you get to talk about dangers to children.
Cullen: Wha - Where did you hear that? That's a lie! Complete, scandalous libel! [...] That never happened! Total fabrications designed to smear my reputation! Besides, that was like years ago, man, and in a whole nother country, and anyway they weren't kids, they were apprentices, which is totally different.
Vegeta: I need you to, AND FOLLOW ME ON THIS ONE... almost kill me. Krillin: Almost ...kill you? Vegeta: Yeah. Krillin: ...And there's no repercussion for this? Vegeta: (beat) I will not punch you. Krillin: Oddly specific.
The central joke of Friendship Is Forever by Slowkings Kyurem is that the Lemony Narrator is constantly denying that Ike and Soren's behavior suggests they're in love with each other at every opportunity. Highlights include saying that Soren was concerned for Ike in a "normal, healthy, un-obsessive way that none of the other mercenaries found slightly creepy in the least" and saying that Soren's response to Ike asking him to run away with him was done in "an entirely chaste and non-eyebrow-raising fashion."
In Hand-Delivered Letter Dumbledore shows up at the Tonks' and Nymphadora blurts out "If this is about the case of dungbombs that was set off in the dungeons last year, I had nothing to do with it..."
Hogwarts Exposed: nudity has nothing to do with sex, and in case you don't believe us we'll keep bringing up sex in relation to nudity over and over again in the course of the next 700,000 words.
From the opening of the How It Should Have Endedparody of Harry Potter, quoth Dumbledore, "Welcome, everyone, to Hogwarts School of Wizardry and Witchcraft, a place, I assure you, is safe for children, and has absolutely no history that might threaten our entire existence."
In Luna's Hubby Luna asks her father how a broom works and when he wants to know why replies "It's not so that I can use it to fly out to find Harry Potter."
Snape: Well, you did declare your loyalty to Hogwarts and the Ministry rather late in the day. Draco: I didn't know that Voldemort had already been defeated. Snape: You spent the previous half-hour hexing parties on both sides of the conflict, while making your way towards the Forbidden Forest. [...] Draco: Alright, I may have been moving in a Forest-related direction. But that hardly means that I was planning to flee to the south of France to spend my life and remaining fortune drinking cocktails in the company of nubile Veelas. Snape: Of course not.
In The Time It Took, Harry breaks up with a guy named Roger because he saw him kissing a woman. Later, Roger shows up drunk at Harry's apartment while Ron is there, leading to this conversation:
Roger: I might have a problem with women, but it didn't mean that— Harry: You also told me you didn't drink. Roger: Fuck you! I am not an alcoholic. Ron: No one said you were, mate, but if you're bringing it up, what are we supposed to believe?
Draco Malfoy: You know who the last girl I'd ever ask to the Yule Ball would be? That Hermione Granger. Not even if we were the last two people on Earth and she looked stunning in her ball gown so that every time I looked at her I got butterflies in my tummy. Not even then.
Man: If you excuse me, I need to do some important work upstairs. And that's all. (cue onscreen text)[ This is what happens when you let Zeromaster improv his lines... o3o ] Man: Nothing suspicious about that. Definitely not downloading porn. Nope, just me doing work upstairs. That's about it. Kyon: Okay, he is so up to something.
The Lemony Narrator of Equestria: A History Revealed seems to feel the need to specifically point out that her biography of King Sombra was not at all copied off from Ponipedia. She still italicizes the source like it was properly cited though, bringing it to even greater attention.
In Flutterspy, a Not My Driver situation results in Rarity and Fluttershy's carriage almost being hijacked by an evil ninja until a secret agent saves them, with Fluttershy mixed up in all the chaos. When Rarity asks what all the ruckus was about, Fluttershy assures her that "Absolutely no ninja fights happened on top of the carriage."
In Nosflutteratu, Garlic Flank Stake just grows garlic. She certainly doesn't do anything with reckless or dangerous with it afterwards.
And again, reassuring everyone that her fake identity is in fact real: "Y-Yes! A perfectly normal librarian who is not in any way, shape or form Princess Luna so nopony needs to feel embarrassed for any behavior they may have committed!"
Twilight's List has Rainbow Dash engaging in this constantly when she's nervous or excited, because she doesn't GET nervous or excited, really! She even does this in her inner monologues, denying how she is feeling even as she shows visible outward signs of it.
One Naruto short story has Anko accidentally mention secreting poison. When Sarutobi points out that he thought she said she coated her breasts with poison, Anko quickly agrees.
Anko: "Yes, of course. It's not like I secrete poison from my nipples or anything! That'd be silly."
This is done seriously in A Teacher's Glory at one point. Despite being Dark Is Not Evil, the Aburame Clan has a bad reputation. They've been accused of feeding their own children to bugs before, so one immediately denies it when Naruto happens across a related subject.
In Vapors there is an international, kunoichi-only diplomacy meeting that includes a hot springs. The Mizukage reveals she has Anbu tasked with keeping Jiraiya and all suspicious frogs out of the city limits. Tsunade brings up that Jiraiya doesn't want to peep on his god-daughter Aiko, who is also present. Aiko objects to being used as pervert-deterrent but Yugito (who Aiko humiliated in a fight a few chapters previously) says:
“Uzumaki, you’re a buzz-kill. I think in punishment, you should be used to ward off Jiraiya. That statement is not merely motivated by self-interest or personal dislike.”
Advice And Trust: In chapter 8 Ritsuko decides to up Rei's drug dose because she does not want Rei developing emotions and getting rebellious thoughts. Then she repeats herself that is her only reason, and most definitely she is not doing it because she is afraid that Rei will take Gendo's attention away from her.
'I don't want to have to factor that into the healing process or the brain scans. I'll leave that until they're done. But I definitely need to up her dose. Can't have Rei waking up one day and deciding she wants to start doing her own thinking. Little dolls don't need to think.' She carefully didn't think about little dolls taking a certain Commander's attention away from her. That had nothing to do with it at all. She was no petty, insecure woman scrabbling for any advantage to get ahead, no.
A little bit, but probably not by grabbing random classmates to conduct "experiments" with. If nothing else, Asuka won't let her do that sort of thing; she's too protective of her friend, definitely a friend, she does not have a crush on Rei Akagi no matter how cute she is now...
Such as the Ree (clones of Rei) talking to canon!Shinji: "And we're totally not eight clones of your mother." "Seriously."
Then there's when Asuka offhandedly mentions to Kaworu that Uriel (Kaworu's sort-of clone) is an Angel now, Kaworu quickly replies "Really? I'm not." Asuka is suspicious but doesn't say anything.
RE-TAKE pulls one off: after killing Arael, Shinji is called into the infirmary to determine whether he suffered mental contamination or not. When asked whether he's seeing things that should not be there, he looked at the vision of Future!Asuka sneering at him and said that he doesn't see anybody. Notice the slip-up? Misato does too.
"What a shame it would be, if, say, these untested, brand-new, powerful weapons were to, say, be fired—purely by accident, of course!—at this space station, if, say, Captain Stadi’s rather reasonable requests would be ignored. I would, of course, be deeply shocked and angered by the gross violation of hospitality, however accidental—shocked, I tell you!—but I would, regrettably, have no recourse but to shelve the inevitable shipboard investigation—only after the most rigorous investigation, of course, but such an investigation would, of course, only turn up the obvious and very unfortunate conclusion that a tetryon array had fired accidentally, and not that, say, I had ordered Dalin Marritza to destroy this space station for your refusal to admit to the crimes committed against the Ocampa species."
In the beginning of the Duelist Kingdom tournament, Pegasus assures the contestants that "this tournament is 100% genuine, and is not in any way an elaborate ruse thrown together at the last minute so that I can get my hands on an Ancient Egyptian artifact."
In "The Other Abridged Movie", we see that Seto Kaiba has "cameras all over Japan" and uses them to spy on Yugi to be always "one step ahead". Even when Yugi is in the shower. When they duel, we get this exchange:
Kaiba: When I'm through with you, you'll going to have to take a shower to wash away the smell of defeat! And I won't be watching you do it! Yugi: ...why would you be watching me? Kaiba: I don't know. I just wanted you to make sure you knew I wouldn't be. Yugi: But I never thought... Kaiba: Good! Because I won't! Yugi: ... why would I think that you'd be watching...? Kaiba: I dunno. Yugi: ... OK...
This one speaks for itself:
Mai: So, Joey, about that dream you had— Joey: I was not wearing a dog suit, and I was not having dream sex with Kaiba!
"Attention, duelists! My hair is definitely not leading you into a trap!"
Marik: "I am Malik Blishtar, in no way related to Marik Ishtar!"