Shin Megami Tensei Strange Journey has an Archangel in a maze warn you about illusion traps in dead seriousness, then he insists that he's helping YOU out, and that he himself is most assuredly not lost.
Borderlands: Dr. Ned is not as good as his totally-not-made-up brother Zed, and they're totally different people. (Exact quote from cutscene in The Zombie Island of Dr. Ned). They actually are different people, judging by the fact that Zed is still alive in the second game.
In Borderlands 2 Rakkman, a bandit who also plays the part of Batman expy, has an audio log that proclaims "My parents jiggled, and squiggled, AND I DIDN'T KILL THEM I PROMISE!" On the surface, it definitely looks like this trope. On the other hand, on Pandora the most common response to "My parents are dead" probably is "So how'd you kill them?"
In RuneScape, when talking to a goblin guarding the secret goblin temple, he says "We not let you in to secret temple that not down these stairs."
Also in RuneScape, when a player asks why all the carts he sees are broken and gets this reply:
CEO of cartmakers: It is unthinkable that our carts might break due to the use of low quality materials, inexperienced ogre labour and usage of enormous quantities of sticky-tape fastenings.
In the Quake series, Quake II has a number of voiceovers layered over one another at the beginning of its intro, which depicts the expository invasion by the Strogg. One of the voices says the following: "Contact with the colony on Mars will be re-established, and has nothing to do with the impending arrival of the mysterious aliens."
In Dragon Quest VII, a Hulkagon tells you that sometimes it's nice to lie in the grass and bask in the sunshine, and invites you to try it. While casually promising that he "won't crush you underneath his massive foot, leaving only a red smear in the green grass to remember you by. Ahh, sunshine..."
In Final Fantasy IX, Marcus is out to steal a Supersoft, necessary to revive his friend Blank, and Garnet agrees to help. Steiner reluctantly gets dragged into this in order to protect Garnet. When Doctor Tot (the character who owns the Supersoft) finds the three in his basement, Steiner insists that there's a perfectly good reason for it, and that they're not there to steal it or do anything else illegal.
An even better example is this exchange:
Steiner: Have you seen a young girl around? Four-Armed Man: What? I haven't seen any beautiful girl with long black hair... Steiner: What did you say?! Four-Armed Man: N-Nothing! And I certainly didn't take any money from her!
Also this exchange:
Vivi Do you know a man named Quan?
Quale I not know that Bigot!!
Final Fantasy VI has Cyan act jittery around the Phantom Train. When questioned about it, he says: "It's not like I have an aversion of machines or try to avoid them as often as humanly possible or anything like that!"
In Rune Factory 3, there are 2 characters who always say things with a reversed meaning. For example, one (who is in a great mood) says "I feel terrible."
Subverted in Portal: "The Enrichment Center would like to remind you that the Weighted Companion Cube will never threaten to stab you and, in fact, cannot speak. In the event that the Companion Cube does speak, the Enrichment Center urges you to disregard its advice." The suspicious denial creates the expectation that the cube will speak, which it doesn't (although at least one other test subject thinks it does).
And a Garrys Mod add-on where, if you look away from the cube, it will make funny noises and when you turn back, it's right behind you. Don't turn and you die. Seriously.
Igor from Quest For Glory IV: "Igor not hear rumors. Igor not know Dmitri's grandfather ran off years ago. Igor not know squid carving eat people who try to open monastery door. Igor wonder if you will verify this rumor."
Darwinia: "This game is not in any way endorsed by SENSIBLE SOFTWARE."note The sound clip that accompanies this (randomly chosen) opening screen is from Cannon Fodder.
Crispin from Psychonauts. "I'm an orderly, you know. I am not an impostor!"
Earlier, Sasha Nein. "Even if you were to take that secret passage over there and sneak into his hidden sanctuary, Agent Cruller would never, ever give you a Marksmanship learner's permit. Never, ever."
Happened in Grand Theft Auto San Andreas. Ryder was going to rob the Pizza Stack, with a brilliant plan to hide his identity... by taking off his cap. The cashier quickly sees through his cunning disguise. Here's the quote:
Ryder: Give up the money! This' a raid! Cashier: Ryder! Not this again! Ryder: It ain't me, foo!
World Of Warcraft: Wrath of the Lich King: After the Wrathgate, a Forsaken Aleric Hawkins says this: "Oh, pay no attention to me. I'm just a messenger. The leader of the Deathstalkers certainly wouldn't be stupid enough to stand here on the dias waiting to be gutted. No need for history to repeat itself." The last leader of the Darkstalkers was the dreadlord whom the Horde kills, and then he just stands there... looking suspiciously unspecific...
A profession quest in Thunder Bluff has you gathering "magic" mushrooms for a recipe the quest giver wants to try. The item description for the mushrooms describes them as "Delicious and completely absent of psychedelic properties."
A Goblin Glider specifically notes that it "usually won't catch fire".
Invoked by the Colonel in Metal Gear Solid 2 Sons Of Liberty. Whenever Raiden asks him about Iroquois Pliskin/Solid Snake, his usual reply is "Do not trust that man. He's not a factor in this simulation."
Interestingly enough, Snake's Revenge was made specifically for the European and American markets, and was never released in Japan (even though a Japanese team designed it). Making its linguistic faults even more hilarious.
In the forward to the recent Touhou Project guidebook "The Grimore of Marisa", Marisa assures the reader "[This] is absolutely not a copy of Alice's grimoire in any way."
Cirno about her hobby of creating frog popsicles: "This isn't playing, this is ice training. I'm definitely not doing it because frozen frogs are cute, or because their cries are annoying, or because it's exciting when juggling them because they might break."
Imperishable Night pulls this off at many passes. Keine hid the Human Village with her power and tells all the teams that there's "nothing around here." Yuyuko blames the endless night she caused (in her scenario) on the last boss, to the last boss's face, and is called out by Youmu. Magic Team does this all night long:
You can also use similar logic to convince an astromech droid to go on a blaster-wielding rampage.
B-4D4: Thank you, T1-N1. Please do not abuse my trust and fire on the guards outside, thereby creating a diversion while I escape with the stolen files.
One Team Rocket agent in the Pokémon games will thoughtfully inform you that there is nothing behind the poster at the Celadon Game Corner. Naturally, when you whup the Rocket agent guarding it, you can pull a switch to reveal their main base.
The tradition is proudly continued in HeartGold and SoulSilver, where the sign outside their Mahogany Town base (opposite what is definitely not a fake tree with a radio antenna sticking out of the top. What are you talking about?) reads "Just a Souvenir Shop, Nothing Suspicious about It, No Need to Be Alarmed."
And also in HeartGold/SoulSilver (don't remember if there was such a line in the GSC originals), upon reaching Azalea Town, a Team Rocket grunt is seen in an argument with some dude, then bumping him and having him run away, and then closing the path to the Slowpoke Well. And when the player talks to him, he states that "Nothing is going on".
In Pokémon Emerald, when you run into Brendan at the Lilycove Department Store, he will specifically state that he wasn't buying any Dolls (a decoration). Without you bothering to ask him...
In Pokemon Black And White, a Team Plasma Grunt in Castelia City guarding one of Team Plasma's hide outs says that there are no other Team Plasma members nor any of the Seven Sages in the building behind him...despite the fact all you did was walk up to the guy.
A trainer who gets in your way on the Village Bridge in Pokémon Black 2 and White 2 refuses to get out of your way unless you beat him in a battle and says you definitely shouldn't try to go around him by surfing across the water below the bridge, because it won't work.
Halo Reach has this line, when Kat thinks of where to get the resources for their new plan:
Kat: "A good place to look might be... I don't know, the nearest nonexistent launch site in the nonexistent Sabre Program, dismissed by three administrations as preposterous rumor... And in which our newestmember was certainly never a pilot."
In Professor Layton and the Diabolical Box, Layton is trying to learn about the title artifact, the Elysian Box. He inquires with one resident of the community of Dropstone, who replies, "Oh, dear! I mean...I've never heard anything about that dreadful, dreadful thing!"
Eggman:(part of recorded announcement) "This amusement park has been constructed entirely out of a sense of remorse for my past transgressions and is in no way associated with any sort of evil plot or premeditated misdeeds." Sonic: ... Well, that's a relief.
A good amount of Eggman's PA announcements are like this: from his urging his guests to leave all their valuables in their vehicles since "in no way will roaming bands of robots will break into [them]" and asking Sonic to pass by the Security Office and not expect to walk into a trap since they "only want to return his keys". Or worse:
Eggman: Welcome to the exotic aquarium. Any water you may notice on the floor is the result of our diligent housecleaning staff mopping, and not evidence of a dangerous leak in the... oh, heck with it. Run for your lives!
James Garret at The Atomic Wrangler wants you to obtain a sexbot, but it's not for him, because he finds the idea of having sex with robots to be disgusting, it's for some of his customers who may be robophiles, the horrible disgusting lowlifes.
In thisTeam Fortress 2 promotional material, Mann Co. claims that they were nowhere near the launch site of monkey astronaut Poopy Joe and had nothing whatsoever to do with the disastrous explosion.
Also, Mann Co.'s seemingly rushed sale of a high-powered rocket launcher was not in any way connected with Poopy Joe's tragic death.
In the Ace Attorney series, the player ( who has been trained to look for suspiciously specific denials in this context after what happened in the previous game) may notice something strange about this exchange:
One quest in Dragon Age: Origins involves tracking down a conman who sold a bogus manuscript to the Circle of Magi; when you finally find him and his retinue of bodyguards, you innocently ask if he's ever done any business with the Circle. The conman replies:
I have no idea what you're talking about, and neither do these large men carrying swords. (Beat) GET THEM!
BlazBlue gets in on this in Noel's story in Continuum Shift while she's pouting over Ragna's treatment of her at the very beginning of the game and her response to said treatment. After the narration mentions how she feels like a little girl with a crush, she immediately breaks out of it and begins denying it outright despite no one else being around. By the end of her denial even she begins doubt what she's saying
Noel: ...No no no. That's not it. That's definitely not it! Definitely not...I think?
Kind of a squick-making thought when you remember Noel is a clone of Ragna's little sister. Then again its been hinted that Ragna, Jin, and Saya are all artificial in the first place so that makes it totally not incest...or does it? ...My brain hurts.
In Katawa Shoujo, Misha and Shizune are most certainly not trying to get Hisao to join the student council just because they would obviously benefit from him joining and therefore have an incentive to try and get him to join.
"I wasn't sleeping and welcome to the Shanghai."
In Shizune's route, Hisao, trying to work out Shizune and Misha's troubled relationship, tells Yuuko that he's worried about two of his friends, one of whom is worried about not seeing the other after graduation, and "It's not Shizune and Misha, by the way".
Defied during Shizune's route before her bad ending Lilly suggests Shizune surrounded herself with people who would agree with her, and Hisao notes she denied doing so. Hisao notes more specific denials are indicators of accusations being true, but says this doesn't apply to Shizune's denial in this case.
When asked about if Herobrine was in Minecraft, Notch said this:
I've publicly told people there's never been any such thing as Herobrine, and that I don't have any dead brothers, and that letting too many animals die in lava is a fool proof way to summon him but that you don't need to be afraid of him. He only means well, he's looking out for you, trying to warn you of the dangers you can't see. There certainly are NO physical manifestations of Herobrine that will sneak out of your computer if you leave Minecraft running at night, looming over you as you sleep with his pale eyes inches away from your face, as he tries to shout at you to wake up. Sometimes you wake up with a jolt, and he's gone, and all that lingers is the memory and faint echo of his wordless screaming. Of course it was just a dream. There's no way a morally dubious ghost with a god complex could at any point decide to haunt the children who play my game "for their own good", as there is NO SUCH THING.
The Glider PRO "Demo House" has text written over the background showing the player where to go. The manhole leading to the secret room has a pointer saying "THERE'S NOT A SECRET ROOM DOWN THERE!"