God of War is basically a deconstruction of the classical greek hero and spartan stereotypes: a person who is defined by using his physical strength to do whatever the hell he wants, seeks revenge for any affront, has a "might makes right" morality and has divine parentage is less likely to be a paragon and more likely to be a violent psychopath hellbent on killing his enemies - at the expense of the whole universe.
Metal Gear has several deconstructions of various cliches and tropes. For example it shows just how much of a tragedy the Fake Defector would be in real life, what would happen to a Tykebomb when they reached adulthood (one is a bitter man almost incapable of making emotional attachments, another spent a good portion of his adulthood being controlled and manipulated), just how mentally unstable or fairly screwed up a real life Quirky Miniboss Squad would probably be (FOX-HOUND, Dead Cell, Cobra Unit) and just how disturbing and yet fairly tragic a real life Cloning Blues plot would actually be.
The issues of the Quirky Miniboss Squad is further deconstructed in a Webcomic based on the first Metal Gear Solid: The Last Days of Foxhound. As are some of the cloning woes and the other issues the game explores, though usually to humorous effect because when it comes to genetics, the author gleefully exploits Hideo Kojima's research mistakes.
At a more meta level, Metal Gear Solid 2 deconstructs a lot of the tropes of video gaming itself.
In an interesting subversion, Urdnot Wrex (one of the first named Krogan we meet) not only starts out as much more mellow than his brethren but goes on to reconstruct the Proud Warrior Race Guys culture of his kind almost singlehandedly, much to the annoyance of more two-dimensional Krogan.
Amongst many tropes it skewered, Planescape: Torment deconstructed the standard RPG trope of your character always being the center of the story by turning the story into a personal quest for identity rather than a standard 'save the setting from Evil Overlord X while most people sit by and watch'. Furthermore, The Nameless One leads the outfit because all the joinable NPCs are bound to you by the Mark of Torment, interlocking their destinies with your own; they could not leave you even if they wanted.
E-102 Gamma's storyline in Sonic Adventure was an unexpected deconstruction of Eggman's robotic Mooks...or more specifically, the fact that Eggman's robots are powered by animals. (Well, technically, Gamma was an Elite Mook, but whatever.) After seeing Amy's flicky in the Egg Carrier's prison chamber, his power source's memories and emotions began to conflict with his programming, eventually leading to his seeking out and destroying the other E-100 models (and himself) to free the animals inside.
All-Loving Hero is semi-deconstructed in stages across all three routes in Fate/stay night as being impossibly idealistic yet not necessarily a bad thing... but only if you can keep your sense of perspective. A handful of other tropes are touched upon in this - such as The Dulcinea Effect - but are generally props for the main point that there is something basically wrong with Shirou.
Kill Zone deconstructs the glorious D-Day style liberation in a hideous situation as it becomes obvious that with a corrupt military brass whom sold out your forces twice, that going in after recovering from a devastating attack on your planet and how putting down the leader will not make things better at all.
Deconstruction, along with subversion, is a prominent focus in the plots of the Tales Series games.
Michael is this character after he's already won. Having "beaten the game," so to speak, he's decided to get out of the game, enter Witness Protection, settle down, and raise a family using his earnings, but he finds "normal" life to be boring. It's implied that him pissing off a drug lord is only part of the reason why he returned to a life of crime, since it's the only thing he really enjoys and knows how to do. The phrase "getting back in the game" is even used to describe it.
Trevor, meanwhile, deconstructs the Video Game Cruelty Potential inherent in many open-world games through liberal application of You Bastard, showing exactly what sort of person would run around causing death, destruction, and mayhem for his own amusement. He is violent to the point of genuine psychopathy, one scene strongly implies that he raped Floyd, and The Stinger implies that he's schizophrenic on top of it. It's not for nothing that he's the only one who takes part in the returned Rampage missions.
Furthermore, unlike past games, V makes no excuses for the fact that its three protagonists are all morally bankrupt. Once they've settled their debt to Reynosa, their only motivation for their continued crime spree is pure greed and self-interest... solving the problem of Gameplay and Story Segregation by demonstrating just who would casually run people over and steal cars without a shred of guilt.
Cody from Final Fight's appearances in Street Fighter deconstruct the Blood Knight. He went to jail despite saving Metro City from the notorious Mad Gear gang, even despite his connections with Mayor Mike Haggar. He's apparently lost the will to fight for any meaningful reason, and claims to do it simply because he wants to relieve his intense prisoner boredom.
Evil Ryu is a deconstruction of the same trope, but from a different approach. Ryu himself is a kind Nice Guy who only wants to be the better martial artist, but within him there's an horrifyingly powerful aura known as the "Satsui no Hado", which can potentially corrupt his whole mind and heart to make him a mindless killing marchine. Evil Ryu is the incarnation of that Superpowered Evil Side, starting in the Alpha games as a cockier version of him and evolving in Super SFIV into a nightmareish and purely evil being; therefore, SFIV!Ryu is shown to be deeply distressed at the prospect of giving into this massive power that will be his perdition. When it almost happens in the Ties That Bind movie, he's driven to a short but very intense Heroic BSOD.
Two different types of Mary Sue are deconstructed harshly during the course of the Kingdom Hearts series. Namine starts out as a Relationship Sue, but it's also shown exactly how one would have to go about supplanting a love interest, and how harmful - possibly permanently damaging - to the hero's psyche and to Namine's own it would be. (Not to mention, also she does it because she's forced into it by others, not juuuuuust because she fancies this dude and wants him for herself). Xion, the so-called 14th member of Organization XIII, is actually not a Nobody at all, but an imperfect Replica, and was never a real member, just a tool. By the end, it's as though she never existed, which is actually quite similar to the fate of many fanfic Sues in her position, but so many of the harmful side-effects are shown that it's impossiblenot to cryat the end.
Suikoden III deconstructs the Mayfly-December Romance of many characters, most notably the Flame Champion as he gave up his immortality by retracting the True Fire Rune in his body so he can age with his loved one, but the act caused his body to break down and eventually die.
Action RPGMetal Walker deconstructs the empty overworld found in many RPGs. Besides your character and a select few NPCs with Mons, no one is outside, even in towns—because killer robots populate the landscape, even right outside buildings. Since you yourself are attacked very frequently, you can imagine why defenseless humans don't go out...
Too may deconstructions to list here, but a particularly important one is the motivation for the antagonist in the Fallout: New Vegas DLC, Lonesome Road. For the Courier, it was an ordinary package like any they'd normally deliver. For Ulysses, it was the package that detonated the nukes stored beneath the Divide, destroying the place he saw as his home, teaching him the power of a single person to reshape the world and sparking off a dangerous obsession.
And if you want the dialog options allow you to play out this trope entirely when speaking with Ulysses.
Fire Emblem: Seisen no Keifu deconstructs Genki Girl and Plucky Girl, since the characters who fitted the archetype in the first generation (Tiltyu and Sylvia) end up meeting really tragic life experiences and are unable to keep their cheeriness in the end.
At the same time, FE also reconstructs the same archetype in the second generation, since the pegasus knight Phee and the thief Patty (and their expies Femina and Daisy) do manage to keep their optimism until the end and earn their happy endings. Yes, they can be sad and/or angry (specially Phee, if her father is Levin), but they don't let it get to them too much.
Fire Emblem Blazing Sword deconstrctucts Attention Whore through Serra, who not only annoys her friends and prospect love interests with her demands for attention and vassalage, but acts this way because she was badly neglected and abused in the Elimine convent where she was raised, so her behavior is somewhat less about her being conceited and more about a massive cryfor helphidden behind her facade. But her own behavior actually ends up pushing almost everyone away (specially Erk and Oswin), who aren't able to see her Hidden Depths until much later.
Fire Emblem: The Sacred Stones deconstructs The Ace with Ephraim. For the first part of the story, it seems he can get through anything. However, when he gets back to Renais, Seth tells him that the citizens are not cheering for his return. They're only happy because Orson's reign of terror is over. Ephraim takes this as the sign that his Leeroy Jenkins tendencies haven't been great for his people and begins to mature from then on.
Not to mention, Ephraim's seeming perfection is the reason why Innes and Lyon show quite the degree of inferiority complexes and covert/not-so-covert envy. In the first case, Ephraim only sees it as normal Friendly Rivalry, but Innes takes it more seriously to the point of telling Eirika that he'll only propose to her after defeating Ephraim; in the latter, it's massively Played for Drama since Ephraim adores Lyon and never ever sees him as inferior, so is struck hard (read: he's driven to tears) when he learns about Lyon's psychological troubles and how a part of them can be linked to seeing himself as inferior to Ephraim.
Additionally Severa and Cordelia deconstruct Calling the Old Man Out. In the Bad Future, Severa didn't take kindly how her mother held an Undying Loyalty to Prince Chrom, the guy whom she once held an Unrequited Love for. At some point, she was both so upset at what she saw as a borderline betrayal to her dad and so scared about Cordelia possibly dying in the war, that she yelled at her mother for it. The result? Cordelia went out to fight, died in battle and never returned home, and Severa was totally traumatised for that. When Severa returns to the past with her friends and she's recruited by the Shepherds, she again questions Cordelia and her throughts on Chrom... but this time it's more of a desperate Jerk Ass Facade, as she's very aware that this Cordelia isn't the same mother she lost (Timey-Wimey Ball and all) and doesn't want to emotionally connect to her only to probably lose her again.
Nowi deconstructs Genki Girl, but from another perspective. What happens when you have near eternal life? Nowi, being a manakete, chooses to spend her days happy rather than depressed by the fact that she will outlive all of her friends: she's very aware that this will happen no matter what and is frequently saddened by that (and shows it, so she doesn't qualify as Stepford Smiler), but she ultimately decides not to waste her time crying for too long.
Ylisse is a deconstruction of a Mary Sue Topia. While it's very peaceful outside of Pelegia sending bandits to attack it, it required many, many years of work to make it peaceful. They also are nowhere near able to fight off Pelegia when an attack is launched against Ylisse an are forced to request aid from their battle-loving neighbors in the north.
Validar deconstructs being Obviously Evil. Nobody actually trusts him even Aversa without having to be brainwashed, which leads to not only everyone being ready for when he inevitably gets Plegia to attack others for the Fire Emblem, but for backup plans to be made in advance for when he obviously goes back on his word or does something else.
When you factor in Zero's origin as the last creation of Dr. Wily the series is also a deconstruction of Joker Immunity, Thou Shall Not Kill, and probably a few other related tropes as well. Because Dr. Wily was not executed after Mega Man 6, or killed in the next game because of Mega Man's Three Laws Compliant nature, he lived on to build Zero, the latter being the cause of the wars in from the Mega Man X series all the way to his own. Then we have Dr. Wiel, the main villain of the Zero series, who was also not killed when captured in the Zero series back story, and came back to wreak havoc.
Dragon Age deconstructs two major fantasy concepts:
The Wizarding School is more of a prison and re-education camp than a school, as it seems to be the only way to avoid devolving the world into a bunch of mage-controlled city states.
Our Elves Are Better is deconstructed, as any race that avoids use of more modern technology is going to get boned — even if they live in the forests.
Not to mention the deconstruction of the resistance, how in spite of Yggdra being not vilified, her weapon has caused more pain and suffering to the empire than what the empire does. And the Sadistic Choice(s) she must make.
And the game takes a good hard look at would happen if you abuse All-Loving Hero and make too much of a scapegoat of him with Nessiah. Yggdra Union has a lot of fun with deconstructionism.
Chrono Cross mercilessly deconstructs Time Travel, specifically the Time Travel used in Chrono Trigger, by asking a simple question: "If you make it so a certain event never happened, what happens to the world, and the people in it, that came to being because of that event?"
The online game You Only Live Once (found here) deconstructs every meta-trope of your average Mario-style platformer (mainly extra lives). Just keep hitting continue...then when it runs out, refresh.
Viewtiful Joe, while in homage to lots of things, has a particularly interesting Deconstruction of Trapped in TV Land, Joe doesn't demonstrate it, but Captain Blue certainly does, the game shows that he got caught up in his fantasy in Movie Land, showing he went insane because he couldn't visit his wife or daughter, and eventually tried to destroy everything, it shows that being Trapped in TV Land sucks, and isn't really something to take lightly.
Far Cry 2 deconstructs Badass with the player character. The enemies attack you on sight, no one bothers to check if you're enemy or not...solution? You kill everything on sight, becoming just like them and racking up hundreds of kills, and by doing that, become the epitome of badassitude with enemies running from you in fear if your reputation is high enough. Of course, this reputation doesn't just affect enemies, it affects friendly people as well, which you need for malaria medicine...
Shadow of the Colossus deconstructs video game objectives as inherently good. Every time you kill a colossus, you see it fall peacefully to its death while sad music plays. Some players stopped playing after a few because they felt they were doing something wrong. You can't help but feel like the invasive villain at times. Especially after you become the final boss.
One could argue that the first Etrian Odyssey is a deconstruction of the concept of dungeon crawling/looting. In their quest for fame and fortune, the "heroes" murder an entire tribe of forest creatures who were acting purely in self defense, murder a man whose only "crime" was trying to develop a way to heal the ravaged world, and putting the entire world at risk by destroying an artifact that was helping the aforementioned world healing. All this, just to complete the Labyrinth and get the treasure at the end of it. This shows that blind, mindless dungeon delving and looting of said dungeons can indeed, and often do, have severe consequences, and the adventurers' sense of adventure and inherent greed make them completely oblivious to such consequences.
Knights of the Old Republic 2 deconstructs several video-game RPG tropes such as how the main character seems to gain power by slaughtering others and how upon meeting you, the other members of your party become entirely dependent on your continued existence. It also deconstructs the Star Wars universe itself, including notions of good and evil and ideas about The Force.
X-COM deconstruct the monster and alien-fighting cartoons popular during the 90's. where you have an elite team of heroes able to travel anywhere in the world to fight cheesy villains and win despite having inferior technology and numbers. Then look at X-COM, who travel the world in a Cool Plane to fight goofy-looking aliens... and suffer a high fatality rate, have barely enough funding, and have to desperately struggle just to get good enough weapons to fight 3/4 of the things that keep coming down.
The Mobile Suit Gundam game Gundam Senki 0081 deconstructs the young vs the old generation. If you are playing as the Federation, the male lead is at a rather old age for Gundam leads (32 years old! That is just screaming for a death wish) while all of the cast on the Federation side are pretty much adults. The Zeonic side consists of young adults who attempt to cause trouble, for a series that usually favors the younger side. The older generation defeats the younger generation in battle.
After completing the first loop of DonPachi, it's revealed that the events of the game have thus far been a deconstruction of the One-Man Army present in many shmup Excuse Plots. The player character, as part of his training, has been fighting against his own army, with his comrades willingly giving up their lives in order to help him become the ultimate Super Soldier. And when you start the second loop, the player character has been doing this same training for the past seven years. Only when he's pretty much slaughtered the entirety of his allied forces is he finally admitted into the elite DonPachi Squadron.
Its second-degree sequel DoDonPachi dai ou jou is a deconstruction of Robot Girls. Set in a future crawling with Element Dolls, robot girls used as little more than slaves (of both the standard variety and...not-so-standard variety), the protagonist embarks on a mission against the forces of Hibachi with the assistance of one of three dolls. Depending on which doll you use, the ending has her choking the protagonist to death and going back in time to cause shit in DOJ's sequel DoDonPachi DaiFukkatsu, falling for him despite him not reciprocating her feelings, or becoming so protective of the pilot that she has to be forcibly removed from the ship. Regardless of which doll, it's clear that your doll has gone batshit insane.
Finally, in DaiFukkatsu, the enemy is a series of giant robot girls, manipulated by Colonel Longhena into destroying humanity.
Each of the romantic routes in Katawa Shoujo features a deconstruction, depending on the girl you pick for Hisao. Not all of them are intentional, but it still counts due to the effects on each relationships:
Rin: Cloud Cuckoo Lander: Feels dissonant with the rest of the world, and falls into depression due to nobody being able to understand her or her art. Becomes self-destructive and compulsive in an attempt to keep up with her art and gain inspiration. One of her Bad Endings implies that she's liable to kill herself due to these emotional problems. Hisao tries to be the Cloud Cuckoo Landers Minder but it seriously affects his own mental stability.
Emi: Plucky Girl: Tries to deal with her issues as much as she can, but this means she can't bring herself to get close to others.
Lilly: The Stoic: Represses her emotions to the point of utter neglecting them, and it's not easy to know what she needs and wants.
Hanako: Declaration of Protection: Eventually gets fed up with Hisao and Lilly coddling her, and the more you try to protect her, the more resentful she is.
Shizune: Spirited Competitor: Is so competitive that she drives away almost all of her friends except for Hisao and Misha. And in her Bad Ending she breaks up with Hisao since she thinks she's driving him and Misha away too.
Command & ConquerTiberian Sun deconstructed Enhance Button. The processing power the A.I. CABAL requires in general and for this operation in particular comes from human brains and the resulting picture looks exactly like one would expect: grainy, except in the parts made up which are very smooth and Oxanna also does not know who the woman on it is, only she's a mutant.
Also, the sequel Cn C 3 deconstructs the concept of using giant mecha in combat; the GDI phases walkers like the Titan out of service because they are way too expensive and, on top of that, extremely vulnerable to some bloke running up and slapping a demo charge on the walker's legs.
Danganronpa deconstructs Declaration of Protection and The Dulcinea Effect: Sayaka Maizono recogonised whiffs of these tropes in her childhood classmate Makoto Naegi and exploited them to her benefit — planning to first worm her way in his affections and make him swear to help her, so she would be able to kill another student and pin the blame on Naegi himself. She would've possibly gotten away with this, had not the guy whom she wanted to murder killed her in self-defense.
As we explore Sayaka's reason to do what was described above, we see that she is a deconstruction of other tropes. More exactly, I Just Want to Be Loved and Attention Whore How so? Her desire for attention has a rather sad background, as she was raised by a single father who also was very workaholic and left her alone all the time. Young Sayaka spent several hours on her own in front of the TV and fell in love with the Idol Singer way of life, thinking that if she became one of these she would be given the affection and love she lacked; thus she worked hard, became a part of an idol group, and was so good at it that she became the Super High School Level Idol Singer, loved and admired by everyone in Japan. Then Monobear exploited Sayaka's massive terror at the idea of being forgotten, showing her a video of what would happen if she didn't leave Hope's Peak: that her group would be disbanded and she'd be totally abandoned by her fans... which ultimately made her snap hard enough to plan killing someone and use Naegi as a scapegoat — and finished when she actually TRIED to kill someone and ended up dead for it. All because Sayaka felt that, if she lost her fans's love and support, she would be literally worth NOTHING.
Super Dangan Ronpa 2 gives us a character who wholeheartedly believes that Hope will always prevail, and wants to inspire those around them... and fails utterly because their mannerisms and methods undermine the very message they're trying to impart.
The Disciples series deconstructs God of Evil by showing what exactly could make a god evil in the first place. Neither of the two evil gods started out evil. They were even two of the nicest gods before their fall. Their villainy is entirely due to the callous actions of the other supposedly good gods.
Kud's route deconstructs Funny Foreigners and other characters whose entire appeal is that they're But Not Too Foreign by having her feel extremely isolated by the fact that, in her true home, she's still treated as though she isn't really Japanese and that all her attempts to be so are hilarious.
At another point, it uses Riki, who is narcoleptic, to deconstruct the Sleepyhead trope and show how randomly falling asleep and being unable to control it can seriously limit one's options, with Riki trying to help out on a farm to provide for Rin after they run away, losing a whole day's work due to falling asleep, and being driven to tears over the fact that he could only ever become an office worker in life since his narcolepsy would prevent him from being able to put an honest day's work in for anything else.
Deponia deconstructs the Kleptomaniac Hero as an aspect of Rufus's self-centered personality; his tendency to take whatever isn't nailed down to further his own schemes is a major part of why he's generally disliked, not to mention that he gets thrown in jail at one point for, you know, theft.
The Hope Bringer is deconstructed and reconstructed in Final Fantasy X. For 1000 years, the summoners acted as bringers of hope by going on pilgrimages to obtain the Final Summoning capable of defeating Sin. Each time this happens, there is a period of time with Sin absent that the people of Spira hopes will last forever called a Calm. The Church of Yevon's teachings also provide hope to Spira by claiming that if they atone for the sins of the past, Sin will never return. Except it's all a huge lie. The teachings of Yevon and the Final Summoning are total hogwash meant to give false hope. The Final Summoning is even more insidious because it is the means of Sin's rebirth, making the sacrifices of the summoners and their guardians (who become the new incarnations of Sin) utterly senseless. Each Calm was essentially nothing but a Hope Spot. The whole system has trapped Spira in what Auron describes as a "spiral of death". Hope Bringer is then reconstructed when Yuna and her companions learn of the spoilered bit above and refuse to go along with it, preferring to risk everything to find a real solution without false hope. It's at this point that the story becomes less cynical and more idealistic.
Valkyrie Profile: Covenant of the Plume is a deconstruction of Roaring Rampage of Revenge and Powered by a Forsaken Child. The moment Wylfred, the main character, gets his hands on an item that can give him power to take revenge on the one who killed his father. Thing is, the thing grows in power by eating souls of the dead. This leads to Wyl killing his best friend in one of the first chapters due to not fully understanding how the item works. Oh, and you can only sacrifice souls of those who trust you. While there are ways to get around killing your allies, you're openly encouraged to kill them (and even need to do so to unlock certain routes)! Also, the person Wyl wants to take revenge on? Not only is it not her fault for why Wyl wants revenge, but she's the only reason he's even alive. Even the best ending has Wylfred's father condemned into that universe's version of Hell because of Wyl's actions.