In Batman: Arkham Asylum, the audience participates in "Scarecrow" sequences in which Scarecrow injects Batman with terror gas that makes him see things. In one of these sequences, the audience is confronted with the screen that appears upon an in-game death, only to find out that it is part of the Scarecrow sequence. Hell, it looks like the game crashes. Scarecrow went from screwing with Batman to screwing with the player.
In the case of The Stanley Parable, the fourth wall exists only for a brief moment at the start.
Professor Layton and the Miracle Mask: In the Bonus Scene after entering the code from Spectre's Call/Last Spectre, Emmy and luke break the Fourth Wall by speaking to the audience, later getting told by Inspector Grosky that they need a permit to do so.
The Legend of Zelda: Majora's Mask: When you first meet Tatl, Deku Link turns towards the camera and shrugs after she practically forces him to let her come with him. This is possibly the only time in the series where Link acknowledges the player.
The Legend of Zelda: The Wind Waker: One of the Tutorial notes in Sturgeons House listed is "Learn all there is to learn in lessons one through nine… And no matter what happens… Do not give up, do not complain, and do NOT stay up all night playing!"
Also, if you manage to land 1000 strikes on Orca during a duel, he will lose count (since the highest the game can keep track of is 999), call you Master, and ask if your fingers hurt, referencing the "Hold" option for L-Targeting.
In The Legend of Zelda: Ocarina of Time 3D, Navi suggests taking a break from playing if you've played for a long time without taking a break. She speaks to the player directly by using your chosen ingame name.
Ghirahim does too, in a sense. During his little ritual with Zelda at the end of the game, he dances around her while humming his own theme song. He more directly breaks it during the first boss fight with him, where he give Link (and by proxy, the player) advice on how to beat him by referencing the Wii-mote techniques required to use certain moves to dodge some of his moves.
Hey, Link, are you getting tired? I sure am. Why not take a break and rest for a while? If you do take a break, be sure to press START and save your progress before quitting!
Talking to Jack Frost or Pyro Jack in the Shin Megami Tensei games often leads them to brag about being famous characters in human video games.
The hero from Shin Megami Tensei: Strange Journey does it too. If you talk to Jack Frost or Pyro Jack, they can ask you if you think they are scary. Turns out you have the unique answer "Mascots aren't scary". When Jack Frost hears this, he says he should have some more screen time and FORCES his way to your party (you can't reject his offer). But if Pyro Jack hears it, he gets furious and attacks you immediately.
In The World Ends with You's bizarro universe, Another Day, speaking to Joshua in Udagawa results in him practically addressing the player with remarks about why the sprites for the main female protagonist remain the same, despite the fact that in the main storyline, she's in her friend's body.
In the same regards, the advice Hanekoma gives Neku about going out to meet new people seems to be equally directed at the players, and this is further enhanced by the fact that the game itself rewards players for turning the game off, or finding friends in wireless mode.
"Tutorial box out."
Vangers goes much further then just breaks the Wall - it reaches out and drags you inside. After you beat the game, the Spector, a vague supernatural entity that was helping...enlisting...manipulating your character in the course of the game, addresses you, i.e. the gamer, revealing that the events of the game are going to happen for real, and that it had caused the game to be created in its past and your present (yeah, they can do that), so that your gaming skills and urge for exploration could be used to make a real Vanger which could break away from its normal repetitive routine and fulfill the Spectors' mysterious goals.
Tank Dempsey from Nazi Zombies. He seems to have quite the talent for it.
Hey Player, drop the chips and get me some ammo!
Power's out...wait-does power even make sense in an ancient temple? Seriously Treyarch? SERIOUSLY?!
''Shangri-La took it to the extreme with his ammo lines:
Hey player, you got about 20 seconds before I show up in your living room and have a few words with you...or until I say another out of ammo line...GET THE HINT?!
Eat Lead: The Return of Matt Hazard. The whole game breaks the fourth wall on a number of levels. The concept itself does away with the idea of even having a fourth wall. It's about a washed up, self-aware video game character trying to make a comeback for a new game generation, only to find out that someone on the development team wants him dead. They even deleted his saves.
In The Secret of Monkey Island, after his lessons on insult swordfighting, Guybrush says "I can’t help but feel like I’ve been ripped off," then turns towards the screen and continues, "I’m sure you're feeling something similar." Later, Herman Toothrot talks to the player on several occasions. In at least one scene, Guybrush then asks him who he's talking to, and Herman replies, "The people watching, of course!"
And complain about the stump/disks joke from the previous game.
When Guybrush falls while climbing a tree, he gets knocked unconscious and starts dreaming. The screen turns red, and he tells the player not to adjust their set.
In The Curse of Monkey Island, when Guybrush "dies," the Grave Digger comments "Funny, I didn't think you could die in LucasArts adventure games."
After that, you get a really funny Fission Mailed, in which the credits roll until Guybrush breaks the fourth wall again by complaining, "Hey! I'm not really dead! Oh, come on, cut it out!"
And if you mock the gravedigger for his fondness of horror novels, he retorts, "At least my hobby doesn't require over a thousand dollars in hardware."
In Escape from Monkey Island, if Guybrush asks a dart player in the SCUMM Bar to try and hit "that guy over there", the dart player will end up throwing a dart at the player and apparently putting a hole in the monitor. Another example of literally Breaking the Fourth Wall.
Done again in Escape. When talking to a group of lawyers, the player can ask to sue over several things.
Guybrush: Let's sue video game companies for making horrible adventure games!
Guybrush: I have no idea why I just said that.
Guybrush also tells the player to be thankful the game doesn't simulate smells, once when entering the Bait Shoppe on Lucre Island, and again when at the perfume stand.
After you lose a multiplayer match on the COG side in Gears of War 2, Chairman Prescott will deride you. He occasionally says: "Reload, refocus, RESPAWN!"
In Drawn to Life on the DS, one of the characters named Jowee wonders how the creator (that's you) sees everyone there. He then thinks that the creator sees them through a white box with buttons, with two windows and controls everything with a magic wand (which is all true). Mari then claims that that's the dumbest idea ever and Jowee agrees.
This entire game, the characters speak directly to you, as their creator. You also have to touch things that will affect the game (usually on request to you, the creator).
In Conkers Bad Fur Day, Conker will ask the player if they understand at the end of every new tutorial and at the end of the game, there is a big glitch where the end boss freezes up as he's about to jump at Conker. He then gets out of his mech and knocks on the screen, asking if there's a programmer in the audience (one communicates with Conker via text at the bottom of the screen). He asks for some weapons (and they warp to a matrix-style weapons area) and to be teleported back to the throne room where he can kill the alien easier. After killing the alien, he realizes that he forgot to ask the programmer to bring Berry back to life and tries to get him to come back with no success.
A minor example from Champions of Norrath, if your character stands around long enough, he/she will ask the player to move on, or take a verbal jab at the player.
Perhaps as an homage to the Metal Gear series' tradition of breaking the fourth wall, Solid Snake is the only character in Super Smash Bros. Brawl who gets to do this. In his first appearance in the Subspace Emissary adventure mode, he stands up from his trademarked cardboard box and addresses the player by saying, "Kept ya waiting, huh?"
Also, if a character is knocked off the screen at the top, they will sometimes bounce off the camera.
In Max Payne, one level has Max shot up with drugs. First he hallucinates that he sees a note that tells him he's in a graphic novel, a format the game uses in place of cut scenes. He exits the room only to find himself inside it again, with the note on the desk again. This time the note tells him he's in a computer game. The latter call stayed the same even when the game was ported to other systems like the Playstation 2.
Also in the first game, there's also a part where you have to enter an elevator. If you shoot at the speaker in the ceiling of the elevator, thus ending the elevator music that plays continuously unless you do so, Max will actually thank the player.
In Max Payne 2, where he walks along a corridor lined with rooms filled with other versions of him, including his character model from the first game (It changed) on which he remarked "I don't look anything like that!"
One was a rather hilarious Woolseyism by the translator about the censorship the game had to go through to get released in the West. Gillian, the main character, calls a "Love Line", and the girl tells him that people are watching everything they say and do. When Gillian protests, she asks him, "Haven't you noticed that every time we try to talk about sex, we're restricted to sly innuendo?" He attempts to prove her wrong, but instead makes a lot of ridiculous double-entendres about "greasing her baking tray", much to his horror. He's finally forced to concede she had it right — in a furious rant, most of the words in which are replaced with "CENSORED".
Gillian can also call the various programmers of the game and get short messages from them, but the only one he can actually talk to is the game's translator. It starts off with casual talk with him and his wife, but after calling him several times, it becomes apparent that their cat goes out rarely, is a whooping 50+ years old and smells rotten and thus is actually a Snatcher, who proceeds to murder them as Gillian and Metal Gear listen to it in horror. Gillian tries to rush to their aid, but Metal Gear says they can't because such a scenario hasn't been programmed into the game and it'd be better to just forget any of it ever happened. Gillian is relieved and thinks the concept of "pussy SNATCHERs" is ridiculous anyway.
At one point, Gillian is allowed to return to his apartment. He cheerfully exclaims, "Wow, I have a home too?" His Robot Buddy, Metal Gear, tells him that he's being silly, to which he sullenly responds, 'I was just trying to make it more exciting for people playing the game.'
During the prologue, there's a very elegant one. Gillian and Metal are in a factory, and Metal remarks that it can hear a sound. Gillian complains that he can't, so Metal tells him to turn the volume up on the TV. The ticking turns out to be a bomb, which soon explodes, Gillian escaping just in time. He stands up, staggeringly, and complains, "My ears are ringing." Snippily, Metal replies, "That's because you left the volume turned up."
Tiny Tiger berates Crash for not including him in the previous video game.
Uka Uka prolongs a cutscene so he can enjoy the dramatic music.
In the first Viewtiful Joe game, Alastor explains the baddies' evil scheme to Joe by reading from the script.
When he reappears in the sequel, he starts to do the same thing; when Joe points out that he's reading from the old script, Alastor apologizes and advises the player to go buy a copy of the original game to find out who he is.
In Red Hot Rumble, when you pause the game, Captain Blue, Sprocket or Rachel will make a remark about the game being paused, such as Sprocket commenting on the fact that you are going to the bathroom, or pausing to answer the phone. But Rachel takes it Up to Eleven by telling you you should go to sleep now if you are playing late at night.
In Final Fantasy V, one of the dancers invites various NPCs from the crowd to dance with her, and ends with in invitation to "You there in front of the screen, you too."
When Krile makes her first appearance, Galuf acts like he doesn't recognize her, with the standard question mark appearing over his head. He then remembers that his amnesia had been cured earlier, and tosses the question mark off the side of the screen.
Several of the insanity effects in Eternal Darkness are based around breaking the Fourth Wall, such as fake error messages, bugs in the game, or a blue screen of death. One of the subtler effects is characters making random attacks in empty rooms; when the character has a gun equipped and happens to be facing the player, bullet holes will appear in the screen.
Balthier, who constantly refers himself as the "leading man" in Final Fantasy XII, admitted that his appearance in Final Fantasy Tactics: War of the Lions seemed to "have more the feel of a cameo role".
Gilgamesh does this in his DLC battle in Final Fantasy XIII-2. "I was starting to worry you'd never download this part of the game, and I'd be stuck in digital limbo!"
And there's also the secret ending where Caius Ballad breaks the fourth wall to mock the player for trying to find a way to stop him and prevent the game's Downer Ending.
Super Paper Mario refers to death as "ending one's game," among a lot of other breakages.
Jaydes refers to returning from the "death" as a "continue."
Then there's Peach's conversation with Francis, the nerdy chameleon. When Francis asks Peach to marry him, the player can have her ask how much money he makes, to which Peach cries, "Who is picking these answers?"
The first Pixl, Thoreau explains his controls, and when Mario asks what the '1' button is, he says "Don't worry, the great being who watches will understand."
The X-Men game for the Sega Genesis asked the player to "Reset the Computer" to finish the Danger Room level. With no in-game switches or controls to operate, usually the player would be stumped... as it turned out, it meant resetting the game console itself.
Mario & Luigi: Superstar Saga has a scene where Bowser is launched into the air, and lands on the "monitor" of the Game Boy Advance, leaving cracks and sliding off.
This gag is repeated in Mario & Luigi: Dream Team, with a fountain flying high and smashing into the screen. (Bonus points for being in 3D.)
Goombella also does it when describing certain enemies and characters. "Oops, I just broke through the fourth wall there, didn't I?"
Occasionally, the character Rawk Hawk will point at the screen and the player. At one point, he even says something along the lines of "Did you forget me?" targeted at the player.
In the second part of the string of final battles, Bowser inexplicably falls through the roof of the final dungeon and decides to fight Mario because he's there. To comment on the fight's Giant Space Flea from Nowhere quality, he says: "Gwar har har har har har! What's a finale without a Bowser appearance, huh? A cruddy finale, that's what!"
The game also realizes that the environments and people in it are made of paper, such as at the end of chapter 5, where Cortez' ship rips through a cliff wall as if it were just part of a set.
The battles also take place on a stage in front of a live audience, the fourth wall between the action and that audience is constantly shattered.
There's at least two bosses that are Dangerously Genre Savvy to know that the audience gives Mario items and power up his Star Power, so they attack the people in the audience to lower their numbers and restore their own HP.
At one point, a little boy NPC says that he's playing Fire Emblem. After the chapter, he says that he's playing the game that he himself is in.
Subverted at the end of Apollo JusticeAce Attorney: We see Phoenix talking to what sounds like the player. He's actually talking to the members of a jury.
However, at the very end of Justice for All, they come very close to doing it—Pearl observes, "This is the first time I get to hear the real you!" The in-game reason is that she's not actually heard him yell "OBJECTION!" during a case, but you're encouraged to yell it into your DS microphone, as it's voice activated (You can still just press "A".)
In Justice For All, examining the patient on crutches in the Hotti Clinic during case 4 prompts "Director Hotti" into talking about how the patient seems to have not even moved since when you were there last. He also states how the man seems to be standing in the same postion all the time referencing the static backgrounds used in the games.
The All-Knowing Vortigaunt Easter Egg Character in Half-Life 2 seems to be vaguely aware of the relationship between the player and Freeman ("Far distant eyes look out through yours.", "Could you but see the eyes inside your own, the minds in your mind, you would see how much we share.")
Fable does this as an amusing Easter Egg. One sidequest involves finding medicine for a young boy who has eaten the wrong mushroom, and consequently spends his days lying in bed and muttering nonsense to himself. If the player hides in the house for long enough (many do, as it's the city guards' blind spot) he will hear the boy say "Nothing is real! We're all just pixels, and our brains are just numbers... whoaaaa..." as well as a reference to the "sandgoose", a nonexistent NPC made up by the developers purely to have something to spread rumours about prior to the game's release!
"Ever get the feeling someone's playing games with you?" "All the time."
In Soul Calibur IV, there's a voice that can be used for female characters in Character Creation. After winning a match, it may say, "Even with the same moves, it all depends on the user."
Serious Sam 2 does this quite often. First, NETRICSA mentions having "a bigger game budget", which leaves Sam confused. Despite this, he goes on to say "this game is full of bugs!" upon meeting the Zum Zum, a giant bee, and after beating it, he says "There will be no bugs in this game!"
Also included is a telephone call to the game producers.
Lampshaded in Kingdom of Loathing: in the entrance to the Clan Dungeon, there is a "notice posted on the fourth wall" explaining that the clan dungeon is subject to change and setting out the rules on multis.
Triple H does this in WWF Attitude. Part of his entrance has him talking to the audience..."for the thousands in attendance, for the millions watching at home...", usually follow by something funny. For the game however his lines are followed by "...and for that one fat ass guy sitting on the couch playing this video game." Take that.
SmackDown vs. Raw has done this twice during the "Road To Wrestlemania" modes on 2010 Santino Marella during the CAW RTWM says your character "Looks like somebody some loser made in a video game,".
Christian's RTWM in 2011 has a scene where Edge says he acted the way he did the previous week to "pull one over on the player" when Christian asks him about this player Edge says "That weirdo sitting right in front of the TV" WHILE POINTING RIGHT AT YOU.
In the Animal Crossing games, if you turn the system off without saving, Mr. Resetti will appear every time you restart and give you increasingly longer lectures about how resetting the game is cheating. City Folk pulls a fake-out the first time you save - Resetti shows up, gives a (relatively) short lecture on the need for saving, then says you saved correctly this time if he showed up.
Deconstructed in The Elder Scrolls III: Morrowind - it's heavily implied through the in-game literature that Vivec attained godhood by realizing that he was in a video game and using that knowledge to edit the situation around him through a process he calls CHIM. The books he wrote directly reference the player (The ruling king who only he can address as an equal), glitches in past games, saving and reloading, etc. It's all covered up in symbols and the dense writing style he uses, though, so it can be incredibly easy to miss.
EarthBound takes this to a whole new level in that you actually defeat Giygas's last form by breaking the fourth wall. It uses the player name that you give to the game when you use Paula's Pray command for the ninth time, saying that the player prays for the kids' safety even though he (or she) has never met them before.
Have a pirated copy or somehow cause the game's anti-piracy system to trigger and try to get to Giygas. As soon as Porky releases Giygas, your console cannot grasp its true form, freezes and may buzz painfully, sometimes bumping into a garbage screen. By this point, your save data is gone. Good job letting Giygas destroy your save data, you could have brought him to the real world, moron!
In Mother 3, some characters attempt to cheesily describe how to perform a certain command (i.e. looking at the map or dashing), and then simply describe it in terms of the game's controls. Sparrows, on the other hand, will simply cut to the point. Then there's the Save Frogs, who talk about preserving one's own memories, which they call "saving." Finally, when you pray at the sanctuary for the first time, you, the player, are addressed directly and are asked to input your name.
Not to mention the player enters the world of Mother 3 at the end of the game. Yes, the player. YOU. And this is before the credits sequence even starts, when the game is supposedly over.
The fourth wall is pretty soft in that game. During the prologue, Lucas' grandfather breaks the fourth wall, then apologizes and returns to gameplay. Later, a Pigmask, very nervously, asks for the name of 'the person pulling the strings... you know, the player!'
All three MOTHER games actually show the player name at the credits sequence if it was given - it was optional in MOTHER.
King's Quest VI: Heir Today, Gone Tomorrow has a unique example: The only way to know which lamp to get from the lamp trader is to watch a cutscene that Alexander doesn't witness. Later, when Alexander is asked how he knew which lamp to take, he simply states, "Just intuition, I guess."
It also has a more "traditional" example elsewhere in the game: On the first screen of the Cliffs of Logic, if you misclick on the steps Alexander will simply land on the ground on his backside instead of dying from the fall. Do it enough times and he'll look right at the player and gripe that you should "Quit making me fall!"
Metroid Prime 3: Corruption may contain a more subtle breaking. Once Samus acquires the X-Ray visor, she glances towards the camera and recoils slightly in surprise, as if she's seeing beyond the fourth wall. Some consider the ending an example of one as well, since she gives a thumbs up, and while it seems to be directed at Admiral Dane denoting that the mission to destroy Phaaze was a complete success, her gunship's windows are tinted and she's moving at too fast a velocity to be seen anyway. Therefore, some consider Samus to be congratulating the player instead.
Metroid Prime 2: Echoes. Upon visiting Agon Wastes for the first time, the player might notice quickly a huge statue of a worm. Scan it and the visor will suggest it's a "potential warning to visitors". That worm was actually a boss. The game just warned you that you're going to fight a huge-ass worm.
While building a communicator in Destroy All Humans! 2, Crypto sings a bit of "The leg bone's connected to the thigh bone" (with more appropriate lyrics) before telling us "I'm not singing the song. I got standards. They may not be high, but I've got them. Besides, we couldn't get the rights." One of the the things NPCs say when they see you is "You were taller in the first game!"
In Atelier Iris: Eternal Mana, Cat Girl Norn gets scared and asks the protagonist Klein to sleep with her in her bed. He refuses, saying "the ESRB would go nuts!" In the end he's a nice enough guy that he at least holds her hand.
Edge: I guess it's possible. What's this game rated?
Ninja Ninja would like you to know that you are a button mashin' motherfucker, and to go take care of this shit while he gets some coffee.
Ninja Ninja broke the fourth wall every chance he got. This Trope remembers him asking if you've seen the T.V. show at one point, and complain about the "endless hip-hop" music that played whenever you met an enemy. There was one trailer for the game where he commented that someone "...dressed up as their favorite character: guy who dies like a bitch." The worst moment had to be when, after Afro Samurai gets grabbed by the Doppleganger and flown into space where they have an epic battle, Ninja turns to the screen and says "You saw that, right? This is some fucked-up shit right here. I'm gonna go get some coffee. Keep an eye on that bullshit for me, will you?"
One of the rewards for collecting all 120 stars in Super Mario 64 is altered dialogue after the final Bowser battle in which he tells Mario to "keep that Control Stick smokin'" until the next time they meet.
The DS remake, being on a system with no control stick, has Bowser telling you to keep the Touch Screen smoking instead.
The flash game Escape from Rhetundo Island has one huge breach for a difficult puzzle. On level 11 you will see flames in top left corner and will immediately attempt to do something with them, while they move in insane patterns. Turns out that they're mouse-controlled, if you don't move your mouse, the flames won't move either. So if you let the guy walk in between two of the flames and slowly drag your mouse to the right, you're safe.
In Tales of Symphonia, there is a large tower called the Tower of Mana, which the protagonists have to unlock as they climb. It can take a while, especially since the group is split into two teams. Eventually, the group have to climb the tower again. Whilst climbing in the second time, a skit is available where Regal comments on the doors being unlocked already. This prompts Lloyd to complain about having to climb the tower again, wondering why they can't use the "Quick Jump" option, leaving Raine and Regal thoroughly confused as to what he's talking about.
This is actually a direct reference to the first game of the series, Tales of Phantasia (below) which had the party's mage, Arche Klein, pull acknowledged quick-jumps in certain parts of the game.
In Devil May Cry 3, Dante kind of did this, LITERALLY at that too. At the end of the intro sequence (before the title screen appears) where a woman's voice narrates the legend of Sparda and his two sons, Dante kicks the screen and it cracks.
Not a concrete example of Breaking the Fourth Wall but, in the Mega Man X series, X throws a victory pose at the player after clearing a mission, just like how Zero throws a thumbs up. Too bad on Zero's part though, he suddenly becomes The Stoic and just turns away to show a Badass Back instead of giving a thumbs up from X5 onwards.
Nina and Max from both Secret Files games sometimes break the fourth wall. Always humorous.
The characters from Touhou occasionally seems aware they're in a video game. It's at times done subtly (the constant references to the adventure as a dungeon crawl in Marisa and Alice'sSubterranean Animism scenario, which could pass as wrong genre savvyness, or Flandre Scarlet telling to Marisa that she can't use "a continue", since in her stage -The Extra stage- the player is not allowed to use continues if he/she happens to lose all the lives) and at others extremely blatant ("I mean, she's still a Stage 2 boss after all.")
Kogasa's appearance as the UFO extra-stage boss may count, as she does "surprise" the players.
Yukari Yakumo is sometimes seen doing this in fanarts, mostly because of her power of manipulating ANY kind of boundaries (technically includes the 4th wall)
Pretty liberal in Kagetsu Tohya. "But... Why has the background music become so foreboding?" - Random thought Shiki has when Ciel is talking about her not being in the play and she has her angry glarey face on. In fact, the whole scene is one big fourth wall breaking complaint about Ciel regarding her low popularity, how her scene for the cultural festival was cut due to time constraints and how little she gets to do in the story this time. She consoles herself with the knowledge that even if she's the least popular heroine, at least she has a custom sprite. Several of the side stories are similarly unkind to the poor, oft abused fourth wall.
In Vampire: The Masquerade – Bloodlines, a cutscene after the player's character first arrives to Los Angeles. After being ambushed by three Sabbat vampires, one of the Sabbat declares "Boys, we're going to have a lot of fun with this one." before facing the camera and saying "Those of you in the first few rows, will get wet!"
If the player is a Malkavian (a clan of insane vampires) the dialoge has a few options for such.
Perhaps the funniest example being if you cheat at character creation to give yourself loads of skill points, the tutorial runner will complain and demand you do it again.
The third Silent Hill game manages to combine this with a Continuity Nod. In a cut scene only accessible to gamers who have played (and still have the save files from) Silent Hill 2, Heather thinks she sees something suspicious in the bowl of a toilet. As she's about to reach in, she suddenly stops herself, muttering that she can't bring herself to do it — at which point she turns directly to the player and asks, "Who would do something so disgusting?" Anyone who's played the second game knows the answer to that.
Silent Hill: Downpour breaks the fourth wall at a few points just to mess with your head and creep you out. When you reach the radio station, Murphy finds his parole papers pinned to the door and has a flashback which reveals why he was in prison. When the flashback ends and the loading screen is displayed, rather than showing tips like it normally does the text simply reads "Was it worth it?"
In the original Punch-Out!!, Mike Tyson says between rounds, "You think the speed of your fingers can match the strength of my fists?"
In Punch-Out!! Wii, Aran Ryan literally breaks the fourth wall if you lose to him in contender mode. He attempts to literally break it again in the next round cutscene in Title Defense, but the ref stops Aran Ryan.
Soda also does this in Title Defense, where he pushes a bottle box at the screen, covering it up.
The VGA remake of Quest for Glory I has a hilarious instance where breaking into the sheriff's safe more than once will give you more experience. However, Otto and the sheriff will wake up to find you doing this and then arrest you for "blatant power-gaming."
In Quest for Glory II, you can quite literally break the fourth wall by throwing things (or a flame dart spell) at the tree that looks like a woman (a rather dickish thing to do). It bounces off and breaks your monitor. Since this is a Sierra game, it's fatal.
Space Quest is notorious for breaking the fourth wall routinely and without reservation throughout the whole series, most often through direct asides and comments to the player through the narration and mockery of your poor skills when you die. A few more notable instances include:
In Space Quest I: The Sarien Encounter (VGA version), if you decide to touch a pool of acid, you get a special, elaborate death scene where the Two Guys from Andromeda, the creators of the series, appear on the screen and detail to you exactly how you messed up, complete with instant replay and on-screen circles and lines drawn pointing to your melted arm. You can also get a similar death scene by walking through a set of lasers, where the Two Guys will again appear and tell you to keep it up since it's amusing.
In Space Quest III: Pirates of Pestulon, you have to rescue the Two Guys from Andromeda from an evil software corporation. While you're making your getaway, one of the Guys turns towards the screen and says "So, how do you like the game so far? Was it worth $59.95?" At the end of the game, you bring the Two Guys to Sierra, the company that made Space Quest. The current CEO at the time then hires them to, you guessed it, make Space Quest.
The entire premise of Space Quest IV: Roger Wilco and the Time Rippers revolves around breaking the fourth wall. Roger Wilco is pursued by the "Sequel Police" for perpetrating unwarranted sequels to his franchise. He uses a Time Pod to travel between various games in the series, some of which don't even exist (such as Space Quest XII). At one point you can even buy a strategy guide to Space Quest IV in the game itself, which gives you some fairly unhelpful hints on what to do (as well as advice on what to do if your computer crashes or freezes while playing, which is all equally unhelpful).
Newer Sierra adventure games use a variety of icons to portray the characters actions. If you click on the hand and then Roger the Narrator will berate you by saying "Hey! Keep your hands off yourself! This is a family game!"
In Space Quest VI: The Spinal Frontier, Roger comments at one point, "Who wrote this crap? Oh yeah, Scott, yeah, well then, yeah, good...good work," Scott being the first name of one of the Two Guys from Andromeda. At another point, the narrator directly addresses the player with, "See what I have to put up with? Maybe they need a narrator over at Myst 2. A guy can dream..."
Space Quest 6 also has several instances of Roger and the narrator talking to each other. And at one point Stellar Santiago also appears to hear the narrator, only Roger tells her it's nothing.
If you die a certain way in Leisure Suit Larry, Larry's body gets dumped into the programmer's bit bucket and recycled for future adventure games.
The game's narrator, particularly in 'Love For Sail' often talks directly to the player. Trying to manipulate certain parts of the female NPCs often elicits responses implying (perhaps correctly) that the player bought the game for that reason alone.
Star Ocean: Till the End of Time arguably breaks the 3.5th wall as part of its plot when your party discovers that their entire universe isn't real and they are all actually exist in a video game created by beings from the 4th dimension. They then proceed to break out into "reality" and kick their own creators' asses.
Happens quite a bit in Shadow Hearts: Covenant. Early in the game, the party runs into a Large Ham masked bandit named "Grand Papillon" (who turns out to be Joachim, one of the playable characters). He boasts about how he's fighting for truth and justice and then the camera cuts to his face, then his chest, then his butt, and finally Yuri standing in front of and facing the camera, holding his arms out in disgust.
And near the end of the game, Joachim is asked by his mentor if he and the party can participate in the "Man Festival". Yuri quickly responds with, "Not in a clean, mega-hit RPG such as this!" After clearing the 50th (?) floor, the quest jumps to the final eight fights. Anastasia comments, "Didn't we just skip about 30 or so floors?"
Also, in Southampton, when Joachim finds a weapon for himself: An annoyed Yuri says, "Don't we usually get our weapons from chests and shops?"
In Secret of Evermore the player meets a crazy old man who rants about how people have no free will and are puppets of a button pressing madman. You (the player, not the protagonist) then get to push a button to determine what horrible fate befalls him.
The MMORPG City of Heroes includes an NPC, Fusionette, who talks about her in-game actions as if she were actually playing the game; she refers to her character's level, talks about going to the "trainer" NPC that players use to gain new abilities, and uses phrases such as "Just wait until my Build Up recharges!" to other NPCs (Build Up being a damage/accuracy boosting ability with a long recharge time). She also appears in one mission where she is not supposed to be, and tells the player, "Don't look at me like that! I had to be in this mission!"
Also in City of Heroes there is a hidden room in the Faultline city zone where Melissa Bianco and Mike Apolis (two of the game's designers) hang out as NPCs and chat with the players.
In Star Control 2, the various alien races address the player directly during the credits, with many of them behaving like actors who have just wrapped up a shoot. Several even go so far as to explain what they expect to be doing in the sequel.
The Jak and Daxter series has some really great examples of this, but a standout is a scene that appears in Jak 3, when the characters meet the Precursors in person. One of them, while the group tries the old "pay no attention to the man behind the curtain" thing, is seen trying to cover the camera with his hand during the scene.
Jak and Daxter pause, stare at the camera, look back at Seem, and continue the scene
In Jak II they have to join a race team owned by Krew. Their contract mentions that Krew owns all rights including game rights.
World of Warcraft taps this one with one of their jokes generated by a human female character using the /silly command. "Do you ever feel like you're not in charge of your own destiny, like... you're being controlled by an invisible hand?"
Same goes for a Night Elf female character, though it's a little more subtle. "Oh, look, I'm dancing again! I hope all your friends are enjoying the show..." (considering the way they dance is pretty stripperific.)
Apparently the folks at Blizzard really like this trope. They actually break it with these two by a Blood Elf female. "Do you think the expansion will make me fat?" and "I'm the girl the ESRB warned you about."
There is also one of the tips that appears when logging into the game: Bring all your friends to Azeroth, but don't remember to spend time outside Azeroth with them too!
Try clicking on a unit you select in Warcraft III multiple times after hearing the whole speech. For example, you can hear the Human Sorceress saying "Click me baby, one more time.".
The biggest one is probably the Crypt Lord, a big-ass spider: "And they say Blizzard games don't have bugs!"
Nearly all Blizzard games use this trope in pretty much the same way. In the Warcraft games, clicking on certain unit types repeatedly results in the unit ordering the player to "Stop Poking Me!". In the StarCraft series, each unit type and character has a short dialog that is triggered by repeated clicking. Most of them stay in character, talking about themselves and their missions; while others break the fourth wall to talk to the character, usually expressing frustration at being constantly harassed by the player, or opinions about how bored the player must be to keep wasting his time like that. A few use quotes from various other pop-culture sources — for example, the Terran drop-ship pilot uses quotes from Aliens, and the German-accented Terran Valkyrie pilot references the "Frau Blücher" running gag from Young Frankenstein. Protoss character Artanis quotes the "Stop poking me!" line from Warcraft. Although the Zerg have no dialog as such, repeatedly clicking on them results in a number of different noises not normally used during play.
"This isn't Warcraft in space!"
In Lost Souls MUD, some NPCs are aware that some of the people found in their world are the puppets of beings from an entirely different order of reality — that is, Player Characters. One has written a book about it.
Sonic Chronicles for the Nintendo DS took the whole wall, stabbed it and hanged it upside down with the ending cutscene. After the heroes exit Nocturne and return to their own world it turns out that Eggman played the heroes for fools and had deliberately helped them to get to Nocturne in order to get all the necessary time to take over the entire world without the meddling of Sonic and his friends. Tails and Sonic then end up having a conversation about how they didn't expect such an ending, how impressed they were of it and how they'll have to wait for the next episode in order to see what happens next. Tails then ends up telling Sonic about the makers of the game, BioWare, and ends up listing the whole cast credits at which point you can, as Sonic, tell Tails that you want to skip it.
Tails would in fact break the fourth wall a few other times before when he constantly reminded you to save your game unless you tell Tails to stop reminding you.
In Sonic Colors (Wii version), when Tails tells Sonic the aliens are called Wisps, he turns to the camera and says "Yeah, I'll just stick with 'aliens' if that's okay with everybody."
In most Sonic the Hedgehog games, if Sonic is kept still for a long time, he will look at the player and tap his foot. In Sonic 2 he also looked at his hand (as if he was looking to a watch), and in Sonic 3 he would even point to the player and then point forward.
Special mention goes to Sonic CD, where if you leave him sitting for 3 minutes, Sonic will yell, "I'm outta here!" and jump out of the screen, resulting in a Nonstandard Game Over.
Characters in The Sims do this a lot as well, looking straight into the camera and yelling at the player if one of their needs gets too low (like if they're really hungry or tired, or really have to use the bathroom).
No More Heroes does this a few times (Travis: And you, with the Wii Remote? Just press the A button...), and throughout the game Travis has little speech bubbles over his head telling you what button to push. The fourth wall is ripped to pieces in the ending of the game ("You'll only jack up the age rating of this game even further!" "Fine, I'll fast-forward through it so you can tell me.") and Sylvia even taunts the players with "Too bad there won't be a sequel!"
And of course, there is a sequel.
Which breaks the fourth wall almost immediately. "Aren't you going to explain what happened since the last game?"
In the RPG/Adventure Anachronox you encounter a man at a spaceport who is telling listeners that they are in a video game and that most of them only have a limited amount of dialog they can say. This is, of course, the only thing he can actually say. One of the listeners, when spoken to, will refute the speaker's claims by saying he certainly had more than one thing that he can say. Again, this is the only thing he can actually say.
In Phantasy Star IV, one of your party members leaves for a bit and flat out tells you not to go after the big bad while he's gone because at this stage of the game, you aren't powerful enough to beat him. Of course, Chaz doesn't listen.
The entire Metal Gear series is rife with instances of breaking the fourth wall. One classic wall-breaking moment in Metal Gear Solid is the advice to contact Meryl by codec by looking up her codec frequency on the back of the game case. In Metal Gear Solid 2: Sons of Liberty, after uploading Emma's virus, the Colonel Campbell construct begins to go haywire and criticizes the player for playing too long and then demands that the player turn off the game. Metal Gear Solid 4 features a fourth-wall breaking moment that advises against the strategy used to beat Psycho Mantis in Metal Gear Solid.
Can't get Meryl's frequency because you threw away the jewel case or lost it? No problem! Contact Colonel times enough and he will give it to you! But, of course, you have to check the Frequency List for it.
Another instance of this in Metal Gear Solid 4, is that part way through the game, Otacon will tell you to switch discs. then, when Snake does not find a disc, Otacon remembers that the game is on the PS3, which has dual-layered Blu-Ray discs.
The colonel telling the player to switch off his console is a reference to the original MSX game, where Big Boss did the same near the end.
Psycho Mantis. During his boss fight you actually have to UNPLUG YOUR CONTROLLER AND PLUG IT INTO THE SECOND CONTROLLER PORT! And, as if this isn't bad enough, until you figure it out, he constantly makes fun of you, comments about the games you've played by reading your memory card and even tells you that he's deleted your memory!
If you lose a number of times, contact colonel and he will wonder if your second controller port is malfunctioning or if you just can't change ports (Emulator anyone?), and he will then provide an alternative solution: Shooting off the masks from the busts of Psycho Mantis in the room. As Psycho Mantis hates his own face, that will cause him to lose his focus and stop reading your movements.
When Revolver Ocelot prepares to torture Solid Snake, after explaining how Snake can rapidly press a controller button to recharge his health, he suddenly turns away from Snake and toward the player before warning that he'll know if you're using an auto-fire controller. And he does know.
Also in Metal Gear Solid 2: Sons Of Liberty, Snake tells Raiden not to worry about Snake running out of bullets and points to his headband and knowingly says "infinite ammo". The player can get a headband that gives them infinite ammo after beating the game.
In Shift 2, the wall of spikes actually stop in the beginning of the game due to faulty actionscript.
In Ratchet & Clank: Going Commando when the aforementioned main characters first land on Notak, they see their target fly away. They then comment to each other that they always seem to be just a bit too late, and ask themselves how that could happen, before turning to look at the camera.
In Tools of Destruction, when Ratchet & Clank meet The Plumber (a recurring NPC in the series) he says that he "didn't recognize them in high-definition".
In the first Ratchet and Clank, Ratchet would turn his head and look at the player when idle. Disconcerting when you were trying to figure out the next platforming puzzle, which was when Ratchet was most likely to be idle.
Disgaea 2: Cursed Memories has many of these, one is pointed out by the main character when one random NPC says that there are multiple endings available by responding "You aren't even trying any more are you?"
The Disgaea series barely has a fourth wall to begin with. Characters are fully aware of their stats and levels, different NPCs try to steal the "main character" spot, and there's surprise when a Bonus Boss from an earlier game turns out to have a role in the main quest. Why, yes, the one Laharl couldn't believe was level four thousand.
The first game also has a beautiful example at the end of chapter four, when Vulcanus says that he's going back to Celestia to come up with a new plan and starts to walk away, then pauses and turns and says, "Got that!? Don't forget it, even if I don't make an appearance for awhile!" Sure enough, he doesn't re-enter the plot until there are only a few chapters left.
This tradition continues in crossover games. In Trinity Universe only the Disgaea characters break the fourth wall. The Prinnies are especially proud of it.
Skate 3, oddly enough, breaks the wall early on, when a cutscene details the Object Dropper dropping objects out of the sky in a cutscene, and Atiba Jefferson comments on it, saying that "Objects are falling out of the sky, man! It's crazy!"
Some of the AI pros say stuff when being faced in a 1-up battle, such as "Who programmed me?!?"
True Crime: Streets of LA The 'hero', a wildly out of control cop, can run over pedestrians. One of his replies? "Don't worry about it, this is just a video game." Made extra creepy, because the bad ending, narrated by Christopher 'Creepy' Walken, has the hero cop thrown from the top of a fifty story building.
"If you really want to be helpful then find a book that tells us how to get out of here!"
"This isn't that kind of game!"
"Game? She thinks this is a game!"
Dmitri Petrovich of the Backyard Sports series does this many times. In the original Backyard Baseball, he says that if the AI improved and there was less chatter, the game would be better. (True thing.) In Backyard Skateboarding, he says "I think we are wasting time" on the choose character screen.
In Simon the Sorcerer the protagonist encounters a group of four wizards; when he talks to them, they pretend they are farmers. But you can point out that when you point at them with the cursor, it says "wizards"...
And when you talk to them, you DO treat them as wizards. You can even tell them about the cursor.
Picking up an extra life in Madworld has the announcers wonder why the enemies never pick up power-ups - "It's like they can't see them!"
Kefka does this in Dissidia: Final Fantasy. When a fellow villain asks him why he doesn't just ambush his rival and kill her without theatrics, he answers: "I wanna have some fun! After all, she's a — good old friend of mine. Mwhehehe!" At the last part, he turns to look directly through the fourth wall, giving the players a knowing gaze since both they and he know about the events of Final Fantasy VI where he met her before.
TECHNICALLY, Kefka sorta does it during his EX-burst. Right before the part where the player has to memorize a three-button sequence, he tells his opponent, and quite possibly you, to "Watch this."
Sometimes he will hum the victory fanfare when he wins too.
In duocedim, Gilgamesh does this when he initiates his ex-burst, starting with a spinning slash and LITERALLY breaking the fourth wall, with his face, specifically.
Also in Duodecim, Feral Chaos' EX Burst ends with him delivering a punch with so much force, it appears to turn off your PSP's screen as if it were a television.
The Dark Spire's final ending concludes with the characters looking up at the sky and seeing the player on the other side of the DS screen. They thank you for your guidance, and you are awarded the title "WINNER".
While the fourth wall in Contact is pretty much swiss-cheesed by the end of the game, the ultimate in fourth-wall-breaking comes at the very end, when the player's character gets fed up with being manipulated and actually attacks you, the player, through the DS's screen.
In The Guild 2 each character belongs to one of four classes: learned; craftsman; self-employed; and outlaw. If you click too often on an outlaw, he/she will reply, pissed: "Stop clickin' me!!!".
Duke: This is it. Let's you and me finish off this bastard once and for all!
One of the endings of the Valkyria Chronicles DLC Enter the Edy Detachment. If you get the worst rank possible, Edy starts ranting about how she deserves a better rank, how the player sucks ("I'm talking to you, sloth fingers!"), and ends the rant by literally telling the player that she is going to re-do the mission to get a better rank. Hilarity Ensues when Homer keeps asking Edy who she's talking to.
In Assassin's Creed II Desmond is using the Animus to view his ancestral memories of Ezio. At the end, Minerva, a precursor to the human race, looks straight at the camera and delivers her message to Desmond, chiding Ezio each time he interrupts saying that the message isn't intended for him (the only person in the room), but is instead meant for the viewer, Desmond, thereby "breaking the fourth wall" of the Animus.
Dead Space 2 has one in the rantings of the increasingly insane Nolan Stross, whom in his paranoid ramblings mentions "him watching".
When boarding the tram with Ellie in Chapter 9, he looks directly at the camera and screams "STOP STARING AT ME!"
The third Gabriel Knight game has a running gag where the player is given options to try some nasty things but Gabriel will refuse to do them, and then he will comment on the player with quips like "You're sick," or "You really are sadistic. You need help." Repeated attempts later would result in "Are you still on that track? Get. Help."
Ristar has a minor break whenever the player loses a life. When you lose the last star that represents Hit Points, it falls down and conks Ristar on the head, knocking him out.
In the final battle of Golden Sun, the first thing that happens is that the Big Bad grows large enough to shatter the screen. Thankfully, this has no real effect on the battle other than following the Rule of Cool.
In The Lost Age, answering "no" to every question up to a certain point results in Kraden going off on Felix and asking if he thinks this is all just a game.
This happens in Fire Emblem of all places. Normally gameplay elements are described in a matter fitting to the world, with the increased avoid in forests being attributed to branches making it hard to hit, and the Secret book increasing skill as a legendary knight wrote down his battle techniques into a book. However, one villager in Rekka no Ken blatantly asks you if you know how to use the R button to look up information.
In Sharin No Kuni Kenichi is generally treated like he's crazy because of his constant narrative dialogue, forever addressing some 'you' character. It's actually a subversion; He's talking to his sister who has been standing behind him all along. People treat him like he's crazy because they are not allowed to acknowledge her existence in any way. On the other hand, Touka also wakes up from a dream that was done from Kenichi's perspective and complains about the confusion that made it seem as though it were really happening. Kenichi has no idea what she is talking about.
Claptrap has a justified breakage of the fourth wall when he explains the functionality of his stash.
Gaige does it regarding her Anarchy stack gain quotes, lampshading how frustrating it is to not reload like normal. Get her Anarchy up high enough and she'll start yelling at the player for breaking the game, or start yelling at the writers to put in more dialogue. Additionally, one of her idling quotes is "LAAAG."
In Zak McKracken and the Alien Mindbenders, the main character loves to do that, and not only him.
In Zeus Master Of Olympus, you can right click people to listen to their quotes. Sometimes, a trader from a not-so-friendly city will say, "Right click me? I'll right click you! You and this city stink and I only trade with you because my leader demands me to."
Played with in Kingdom Hearts II. Stitch crawls on it, licks it, and stands on the Command Menu, as well as Sora's HUD, or, to be precise, on the Drive/Summon Gauge.
In Kingdom Hearts 3D, if you poke or pet a Ghostabocky, it occasionally tries to eat the hand cursor, only to spit it into the screen with disgust shortly after.
The lesser known PS1 fighting game Zero Divide has an instance of fourth wall breaking, when the announcer asks if the player is trying to break the controller if buttons are mashed repeatedly. This instance can be seen here: http://www.youtube.com/watch?v=a4ucvOVJjpI (Cut to 1:28 when the video has loaded enough).
Rayman has the eponymous character look towards the screen and attempt to contact the player through motions and gestures if left idle while standing still or hanging from a ledge.
At the entrance to the Heavenly Jade Imperial Tower in Bunny Must Die! Chelsea and the 7 Devils is a red gate and a switch where you place your yellow gem, which naturally doesn't do anything. Cue message stating that it isn't a glitch, and Bunny wondering what the voice she just heard was.
In League of Legends, every so often, one hero Mordekaiser responds with "You only need to click once... fool!" when given the order to move.
This is more a No Fourth Wall as almost all the champs have a similar line.
Some of the units in Company of Heroes will break the wall if you click on them enough. A few examples:
British Infantry Section: Oi! Get your filthy hands off the mouse!
Panzer Grenadiers: Clickity, click. Clickity fucking click. Fucking scheiße...
In Celadon Mansion in Pokémon Red and Blue, you can talk to a programmer, graphical artist and script writer who worked on the game. They talk to you about your Game Boy and one even remarks "I drew you!"
Looking at the computer the script writer is at mentions "Better not look at the ending!"
Interacting with the in-game models of the development team is done in every game. In Ruby/Sapphire they're on vacation in Hoenn. In Black and White, you're even able to battle one of them.
Fallout 2 has LOTS of these. Bartender of the parlor: "Are you OK? It seems consuming so much alcohol Z had some effect on you." Chosen One "I'll pop out of the conversation one second and check my max hit points." Chosen One: "Bastard! Wait till I load my last save!"
Deadpool carries over his habit of breaking the fourth wall into Marvel vs. Capcom 3. When he's knocked out, he yells out "YOU PRESSED THE WRONG BUTTON!", referring to the player controlling Deadpool. Upon winning. he'll also scold the player for sitting on the couch and being lazy while he has to do all the fighting. There is another one where he asks if the player was recording the fight and chastises him for not doing so. Finally, his Level 3 Hyper Combo has him assume a girlish pose and walk toward his opponent with a pink aura and hearts surrounding him for a few seconds. If he is attacked in this state, he'll jump up, grab his health bar, and whack his opponent in the head. He then grabs his Super Meter, winds up, and knocks his opponent sky high.
He also shouts "Hey I freaking love Street Fighter! Autograph your spleen for me?" if he is on point against a Street Fighter character (Ryu, Akuma, Chun-Li and C.Viper). If landing the killing blow against one of these, he will say : "I get the cover of the next Street Fighter for this, right Capcom? Right!?" Also, in his ending, he says "I'd invite you to party with me, but you'll just have to make do with the points you got for beating the game. He then accidentally destroys a city, causing the cops to put out an APB for him and his accomplice, "The Player."
It'd be easier to list the few instances where he doesn't break the 4th wall.
If you fall far enough to hurt yourself, but not far enough to die, The Saboteur will shout things. One of them is "Stop that!"
There's a minor example in Dead Rising 2. The player can get Chuck to wear various outfits you find in Fortune City, and he comments on most of them with stock lines like "Killer", "Smooth", and "Nice". Make him crossdress, though, and while sometimes he'll deadpan "Pretty", he'll also say "Um...Seriously?", and "If you say so..."
Whacky Wheels has a literal example of this. If you run into certain obstacles at high speed, your character will fly out of their little go-cart, hit the screen (leaving huge cracks) and slowly slide off.
The camera viewpoint moves across the interior of the shaman's hut as he chants to summon a juju spirit. When the camera is on his face, he opens his eyes and screams at the sight of the player looking at him.
"You are so strange! Your clothes. That powerstick you hold in your hand. I have never seen a juju like you before. What is this magic box you watch me on? [Presses his hands to the screen so you can see his fingers flatten themselves on the screen.] It is clearly the most important thing in your hut! You do me great honor to watch me on it...."
In X-Men Legends II: Rise of Apocalypse, every character has a couple of lines when they're idle for too long, and several are directed at the player, like Bishop's "Hey you! Yeah, you! What are you doing that's so much more important than this?"
Yo-Jin-Bo does a pretty good job of smashing that wall, too. The guys like to tease Mon-Mon about "not being one of the characters you can get at the end of the game", and his response is that he has an Image Song and has spent too much time reading his lines to not be a "captureable character".
The Simpsons Game is just layers of this. At the finale of the game, God asks you for his guide book back, which then zooms out to Ralph Wiggum playing on his TV. Ralph then turns and just STARES at you.
In the Runescape 2011 Easter event, a squirrel named the 'Antipodean Squirrel', is angry about how the Easter event is Northern-Hemisphere-Centric, and about how it is Spring in the northern hemisphere and how it is autumn in the southern hemisphere and it is not fair to no autumn event. (One responce is to tell him to stop breaking the fourth wall, which the response is 'Yeah, likeyou stay in character all the time!')He is angry how one half of the world is being left out. And his way of solving the problem is to 'Stand here... and keep shouting'.
The first game has the Professor refer to the game interface after you capture the angry Rhydon — "By options, I don't mean fooling with some text settings, I mean consider what we might do!"
Also, Magikarp's Pokédex entry in Platinum, and Pokémon Black and White says that if it lives for many years, it can leap a mountain using Splash, but that "The move remains useless, though."
Mega Man Battle Network 6: There's a Navi Customizer program called Humor, in which we can trigger a conversation between Lan and Mega Man (and occasionally someone else). In one occasion, Mega Man asks whether Lan is being "operated" by an unknown guy. Then Lan somehow recognized (indirectly) that he's a guy in a 6th installment of a game. Detailed here.
The art dealer from Little King's Story: Upon approaching him, he says "You in front of the TV playing Little King's Story!"
On the last level, Bubsy asks, "are you still playing this thing?".
In the space action sim Tachyon: The Fringe, when entering a console cheat code, the main character will start taunting the player for his lack of skill.
In the game Castle Shikigami III (full name Castle of Shikigami III), the characters sometimes break the fourth wall, such as Reika from Time Gal.
Reika also mentions the game Time Gal, then asking the players.
Reika: No arrows show up on the screen, so I don't know which way to go. Hey, don't you guys playing the game think so too?
And it gets more odd; Reika metions THE PLAYERS, then TELLING THE PLAYERS TO POWER UP THEIR STRENGH at the begining of the last boss.
In Destroy All Humans!, at the opening choice options screen on the mothership, if you fail to make a decision and leave the screen idle, Pox will sometimes say a random thing to you relating to the situation (i.e., "Well, it's your electric bill. You could have thought to turn the console off. Haven't you ever heard of global warming?" or "May I remind you that the name of this game is "Destroy All Humans", not SCREW AROUND IN THE MOTHERSHIP!").
In Persona 4 there is an NPC that mentions the ever-so-wonderful Square button that has the power of teleportation.
Housewife: With just a press of the Square button, you can come and go as you please... Ah, the wonderful Square Button.
This comes up a lot during the Sly Cooper franchise, with dialogue such as: "Bentley, how do I climb ladders?" "Simple Sly. Just press the circle button."
The Matrix Path Of Neo has a bizarre example during Neo's fight with Seraph, the bodyguard of The Oracle. It starts out like in the film, has them take the fight outside where they battle atop numerous wooden poles that are being lit on fire... and then takes them into the real world. No, not the "outside the Matrix" real world... I mean our real life world where the Matrix is just a work of fiction. The two crash inside a movie theater playing actual live action clips of their fight scene from the The Matrix Reloaded even as the two continue to fight in front of the screen, with one movie-goer heckling the two the entire time.
As a series about console wars personified, it's only natural Neptunia would break the fourth wall. For example...
Kid Icarus: Uprising is guilty of multiple counts of fourth wall breaking; talking about various story cliches, referencing various other Nintendo titles as well as its sister series, and a literal case after Chapter 9, where Hades tears through the fake credits.
After beating Samurai Shodown 2, if the player chose to play as Wan-Fu, he breaks the fourth wall by telling the player he doesn't have a story ending like the other characters in the game do.
The DigiPen student game Perspective does this rather spectacularly in its finale. After escaping the Arcade into a meta-reality, the character escapes THAT meta-reality through a machine labeled "Perspective". From there, there are a series of portals that simply loop back on themselves. The only way to escape this is to pause and quit the game. The player is presented with their desktop, which turns out to be another set of screens in the game. One falls over, revealing another portal. You, yourself, travels through the final portal, revealing the game's actual menu.
In Lollipop Chainsaw, Juliet is able to see the bosses' info cards, and sometimes interacts with them (like responding to Zed being an animal abuser, or slicing through Vikke's info card).
Grand Theft Auto III has a sign saying "you weren't supposed to be able to get here you know" in a difficult to reach location.
In Jazz Jackrabbit 2, if Jazz was kept idle long enough, he would look at the camera and yell to the player, "Hey! HEY! Come on, let's go!"
At the conclusion of Panzer Dragoon Saga, the dragon reveals to its rider, Edge, that the dragon is not, as the other characters had until now assumed, the 'Divine Visitor' who was prophesied to save the world. Instead, the dragon then turns to the camera and addresses the player by name (which they had entered back at the start of the game), stating that they, the one who has been controlling Edge's actions, are the Divine Visitor.
Commonly happens in Rewrite, as it often pokes fun at RPGs in a very meta way. For example, in one scene Kotarou starts telling himself about a quest Kotori set him on, and then informs the 'lazy bums in the audience' that not completing the quest won't affect Kotori's Relationship Values. Later that night, a man comes to Kotarou in a dream telling him that he's the autosaver man and apologises for slacking on his job, telling Kotarou he's worried that the last couple of times the 'Autosaving!' sign came up in the bottom right-hand corner no saving actually occurred. This time, Kotarou is mystified and has no idea what he's talking about.