Otacon: That blade in his hand is called the Master Sword, also known as the "Blade of Evil's Bane". He also has a whole arsenal of items at his disposal— bombs and arrows, a shield, a boomerang and a Clawshot. He's a force to be reckoned with. Snake: Gear is only useful when it is used at the right time and place. Just lugging a ton of it around doesn't do you any good. Otacon: .... I... uh... I wouldn't be talking if I were you, Snake. Snake: What's that supposed to mean? Otacon: You tell me, Mr. Utility Belt. Snake:(grumbles)
While most likely a developer oversight, when you are captured in Knights of the Old Republic, you can lie and say you don't care about Carth/Bastila during a torture session but the torturer will claim it is an obvious farce because you traveled half way across the galaxy with them. Considering he was the mentor of one of the people he is torturing...
If you keep Bastila and Mission in your party long enough for a cut-scene, Mission will ask Bastila if she's ever used the Force to, say, trip up someone who was annoying her. Bastila is appalled, claiming the Jedi do not stoop so low. When Mission keeps pushing, she suddenly gets swept off her feet by a Force push.
KOTOR II has this meta-example from its own endgame:
Sion: You... seek to erode my will. You will not succeed. [You have eroded Sion's will, reducing his Will saves, Constitution, and Wisdom.]
OWI said in the manual that they did a thorough investigation of Sobe's history of human rights and such before "proudly" advertising for them in-game.
Kingdom of Loathing example: In the "South of the Border" zone, one of the encounters is a cock-fight. You can bet on the favorite, bet on the other one, or walk away. If you choose to walk away, you get this text:
This flagrant display of cruelty to living creatures disgusts you. You decide to head back to the Icy Peak and eviscerate some more Yetis.
In Dissidia: Final Fantasy, Kefka dismisses Sephiroth as "just another sadist with a god complex. Like THAT's anything special!" Being the story's Meta Guy as well as an honorary "sadist with god complex" himself, Kefka seems fully aware of (and amused by) this hypocrisy.
Also in Dissidia, Quistis is the ingame tutor for equippable items, and stresses its importance. When you realise that her origin game doesn't make use of equipment outside of weapon upgrades...
In BioShock 2's Multiplayer mode, noticeably overweight bourbon magnate Buck Raleigh sometimes has this to say while researching a fallen enemy: "Gotta be fit to survive down here, friend!"
A cute example of this trope can be found in Professor Layton and the Unwound Future. Both Layton's apprentice Luke and his adopted daughter Flora strongly dislike being away from him; Luke feels it's his duty to always watch Layton's back, while Flora has separation anxiety. At one point in the game, Layton disappears for a brief period.
Luke: I hope we find the Professor soon... Flora: Poor thing! You're just lost without him, aren't you, Luke? Luke: You're a fine one to talk!
Tali: 67: holmium. Very reactive, very magnetic! Garrus: You know, turian parties don't usually end with someone reciting the elements. Traynor: 68: erbium. Atomic weight: 167 and change! Tali: Right, my turn. 69.... Jack:In your dreams! Tali: What? I don't get it. Traynor: I'll explain later. Garrus: It's thulium in case anyone's still interested. Turians have trace amounts of it in our skin. Helps protect from solar radiation. Tali:Neeeeeeeeerrrrrrrrrd!
There's an instance of this that's fairly easy to miss, early on in Apollo Justice. The defendant in the first trial remarks " As I expected. Your eyes and ears are as sharp as your hair." to Apollo... but, if you recall, the defendant is Phoenix, who's rather legendary in the court for having spiky hair.
He probably meant it as a compliment, given how proud he was of his own hair.
In the Portal series, GLaDOS often tells you that you're adopted and fat. Once Wheatley performs his Face-Heel Turn in the second game, he says the same thing, but GLaDOS responds with this:
GLaDOS: And? Wheatley: What? GLaDOS: What, exactly, is wrong with being adopted? Wheatley: W-what's wrong with being adopted? Ummm... lack of parents— GLaDOS:[Whispering] For the record, you are adopted, and that's terrible. Just work with me. [Normal voice] Also, look at her, you moron, she's not fat.
When you reunite with GLaDOS she calls you a monster for killing her, even though she's the same silicon sadist who tried to kill YOU - unprovoked, at that - in the first game.
Tatsunoko vs. Capcom: "I guess even kids can become heroes in Japan. That must be one crazy country." Well, then, Frank, how about your own country?
In Ultima VI, you have to determine who is the most humble person in New Magincia (which has humility as its Hat) in order to receive the Rune of Humility. Practically everyone will boast about their humility and list the luxuries they've given up and the lowly and humble tasks they've taken up, to prove how exceptionally humble they are. The one exception is the fisherman, who doesn't care about it but is fairly sure he's not particularly humble. You can probably work out the rest.
Comic Book Guy: Videogames, what a waste of money. Now to go online and bid $1,000 on Itchy & Scratchy corn-cob holders! A terrific, terrific expense.
Quite common in the Postal series. For instance, in Postal 2, the first hate group you come across is "Parents for Decency", a group of parents who are opposed to violent video games. They attempt to stop the creation of such games by storming the Running With Scissors offices with guns, after that point they will open fire on the player without provocation, and much later in the game you can find a group of them playing arcade games in the mall.
Another group, "Parents Against Graffiti", is not seen in the game except for, you guessed it, a graffiti tag identifying them.
In the Pokémon RPGs, Red, Blue, Yellow, Leaf Green and Fire Red, there are SNESs situated beside TVs in the Celadon Department Store. When you examine one of them the text reads "An RPG! There's no time for that!"
Kenji says "as expected of blind people" in reference to Lilly. Hisao then asks if it includes Kenji, and Kenji points out that he's only legally blind.
An exchange with Misha and Shizune's father, Jigoro.
Jigoro: And another thing, you do not have to be so loud. I do not like being shouted at. Misha: What? Shouting~? I'm not shouting~! Hisao briefly notes how hypocritical Jigoro is being Misha: Ow~! My ears hurt~! Jigoro: WHY ARE YOU SHOUTING?
Jigoro also scolds Hisao for making assumptions about him, yet he constantly makes assumptions of Hisao being, for instance, a glue-huffing delinquent.
In Act 1, Shizune scolds Rin for sleeping on the tables of the art room. In Shizune's route, she and Hisao have sex in the Student Council room.
Glottis: It's not just a job, it's what I was created to do! If I get any farther away from a car than this, I'll get sick and die! It's like I'm not happy unless I'm breathing in the thick, black, nauseating fumes! Manny:(takes a very long drag of his cigarette) I can't imagine...
She sometimes comments negatively on other female characters' choice of revealing outfits, as well on Joe (and Hwa Jai) for wearing only boxers. When she is criticized for (or reminded of) her extremely Stripperiffic outfit, she says that her case is different as hers is "traditional garb passed down from [her] ancestors!"; however, the fact that she is ocassionally seen wearing something very revealing outside of the ring doesn't help her case.
In Transformers: Fall of Cybertron, Megatron demolishes one of Starscream's monuments to himself, citing it as an example of fruitlessly wasting Energon. All the while other Decepticons tear down more of Starscream's statues. Not mere seconds later, an even bigger statue of Megatron is flown in and set down smack dab in the middle of the courtyard where the scene takes place. Given the game's rather G1-esque spirit, this is almost certainly deliberate.
Batman: Arkham City has a bit of Enemy Chatter where a crook says the first thing he's going to do when he escapes Blackgate Prison is get a beer, explaining that he's in for DUI. Another prisoner admonishes him not to go driving while drunk or he could kill somebody; when asked why hes in Blackgate, the second prisoner says, matter-of-factly, "Manslaughter".
In Dynasty Warriors 7: Empires, if you manage to continually defeat Dong Zhuo without capturing or killing him, he will eventually say this line if you encounter him one more time:
Dong Zhuo: You are a villain that must be eliminated! I will be the person to do it!
Comically ironic, given that he is a major villain himself.
In The Pandora Directive, Tex Murphy comments on a book titled "Men are Imbeciles, Women are Erratic," saying, "The author generalizes too much, and I think all people who generalize are idiots."
The game has plenty, much of it coming from Handsome Jack. For instance, he'll call you a child-killer for killing his daughter Angel at her request in spite of the fact he's been known to terrorize families himself. It's heavily implied he killed the children of one of his lackeys.
Another, somewhat more subtle one is in Opportunity—obviously Handsome Jack has been using the city very much as self-propganda, depicting himself as the conqueror of Pandora, while also name-dropping Hyperion weapons. Amusingly, in the mission where you can get a 'history lesson' about Jack, the speaker glorifies Hyperion and claims Jack conquered it with Hyperion weapons, suggesting them to be the best that could be had...when he's clearly shown in every panel using Jakobs pistols, a gun type which does much more damage than almost anything of the same size that Hyperion could manufacture. A couple of his statues in Opportunity also has him carrying an exceptionally powerful and extremely distinctive unique Jakobs sniper rifle.
More Handsome Jack, again—given how much he hates swearing from others (considering it 'verbal pollution' and worthy of a death sentence in opportunity), he's quite the pottymouth, ranging from childishly immature to just plain angry cussing. Getting him mad is half the fun at some points.
One not from Handsome Jack: occasionally, you will run across midget versions of Nomads. Nomads hate midgets (using them as literal Bulletproof Human Shields by strapping them to their riot shields) and using pejoratives like "midget lover." In spite of this, you will hear the midget nomads shout things like "You're worse than the midgets!" What makes this especially hilarious is that normal nomads have incredibly deep, Fat Albert-esque voices, while midgets have squeaky, high-pitched voices... and midget nomads have the high pitched voices with the 'deep' timbre, which just becomes hilarious.
BlazBlue: In Rachel's gag reel, the several hundred years old vampire girl accuses Ragna of being a paedophile because she's accompanying Platinum in a restaurant (it's actually that she's a walking, talking plot MacGuffin). However, it's heavily implied in the end of the reel (and in several other points in the story) that she fancies him.
In another example, also from a gag reel wouldn't-ya-know, Litchi lectures Tsubaki on how a woman should only show just enough skin to pique a man's interest, but generally try to be covered up. To wit: this is Tsubaki◊ and this is Litchi◊. Tsubaki herself calls her out on this.