During the Fragile Cargo mission from Ace Combat 3 Electrosphere, you have to prevent an airplane packed with anthrax by a bunch of terrorists from crashing against some huge chimneys that look a bit too much like the World Trade Center. In order for that blimp to safely land on water and not crush the chimneys, the player must shoot the chimneys in the way.
The original Command And Conquer Red Alert 2 packaging had artwork of the Soviet attack on New York, with the burning Twin Towers prominently displayed. Needless to say, said packaging was pulled off the shelves after 9/11.
The first Soviet mission sends you to destroy the Pentagon. The third has you guarding a superweapon built right next to the Twin Towers. Yes, you can destroy the towers with your tanks (they are better utilized as garrisons for your conscripts). To make matters worse, the game rewards you for this by dropping boxes of cash for you to pick up once the towers are destroyed. Later patches would change the names of these buildings (and other famous monuments) to generic ones. And then fan mods reverted the names because as we all know, people don't like censorship.
In Red Alert 3, the main tank of the Empire of the Rising Sun, which is Japan, is called the Tsunami tank.
In the opening to Combatribes on the SNES, the center of all evil in New York is run by a group called Ground Zero. Awkward.
In one of the Aero Fighters games on the Neo Geo, a level that takes place in New York City lets you blow up the World Trade Center towers... with a plane... and you get rewarded with money for doing so.
The first level of King of the Monsters 2 has the Twin Towers, which can be thrown or destroyed for giggle.
In the opening levels of Deus Ex, set in NYC, the WTC towers cannot be seen in the distance due to an engine limitationnote basically, the skybox for any given level, rather than showing the full 360 degrees of art, only show 180 degrees of it and then mirror that for the other half; the half that is shown for the NYC levels just so happens to be the half that doesn't include the towers. The in-game explanation? Terrorists.
The fact that one of the main plots portrays a government orchestrating terrorists acts to get pretense for freedoms-curbing legislation doesn't help either.
Then there's the Statue of Liberty being C4'ed by terrorists, which makes the absence of the WTC even more disturbing. On the other hand, Statue of Liberty has been decapitated by French freedom activists who have deliberately chosen such act to perform a symbolic action without any human casualties. Although it is strongly implied that the main villains framed them for it, which makes it possibly more disturbing.
Another one from Deus Ex: One of your missions reflects the in-universe gas prices. The gas station in question has something in the lines of $4.50 a gallon (this was back when gas was still under $2/gallon). Now take into consideration that average price of gas now in the U.S. has reached that point...
American shows referring to the price of gas are always Harsher in Hindsight for British audiences. The price of gas in the UK, as of 2012, is $12/gallon.
One of the possible things that could happen in Sim Tower was for terrorists to plant bombs inside your tower, which you then have to stop. Ouch.
The Electronic Arts game Urban Strike was set in the year 2001, according to the intro. A cutscene in which Malone's laser fires and blows up part of the World Trade Center is shown right before the seventh campaign, which takes place in New York City. When you reach your destination in the mission to rescue the survivors, there is a huge smouldering hole in the side of one of the towers. If you fail the mission by incorrectly defusing the bombs that have been set in the towers, the whole thing comes crashing down. The fact that some crackpots do believe that placed explosives brought down the Twin Towers makes this even harsher. It originally came out in 1994, a bit Too Soon after the 1993 car bomb attack.
In Final Fantasy V, there is a forked tower (meaning it is one building on the bottom, but splits into two) that two party members must take each side.*
The 1990 Neo Geo game The Super Spy ends with a warning on the increase in power of terrorism, complete with an image of the Twin Towers in the background. Then come 9/11...
The Neo Geo arcade game Sonic Wings 2 (aka Aero Fighters 2) features New York as the backdrop for level 2. While the Statues of Liberty can be shot for a powerup, there is no physical damage, though this is not the case with BOTH twin towers. Not only that, but there's money inside each! Paid to destroy the Twin Towers. Golly.
A rare example of it happening before the game is released, so the moment really only happened to the developers: Metal Gear Solid 2 had a scene showing Arsenal Gear crashing into New York, including a detailed scene where the towers were destroyed. It was supposedly going to be one of the best scenes in the game - but just before the game was set for release, 9/11 happened, causing them to hastily edit the scene and leave it rather disjointed.
More specifically, the landfall of Arsenal Gear purportedly destroyed all of New York City's financial district. The prow made it so far inland as to toss the protagonist and his nemesis onto the roof of Federal Hall, which, as anyone who has been to Wall Street knows, is quite removed from the coastline. Early concept art shows the devastation, with the south end of Manhattan reduced to smoldering rubble. The final version cuts away to black as Arsenal Gear approaches the Brooklyn Bridge, then shows the mobile base already at rest at Federal Hall.
The 2010 oil spill off the US coastline makes one wonder when BP is gonna put up a Big Shell over the Gulf of Mexico...
The game also introduces the main villains of the series with the Nebulous Evil Organization of the Patriots, which has been in full control of American politics apparently for well over a hundred years with the ultimate goal of stripping the population of its civil liberties and turn them into mindless slaves that are completely oblivious of their control. Given that the game was released in November 2001, any similarities to the PATRIOT Act and its aftermath are probably completely coincidence.
Way back in the first Metal Gear, released in the late Eighties, Snake must reach Metal Gear by crossing an electric floor. All the other electric floors in the game have had panels which can be shot with missiles in order to prevent Snake getting zapped; this one had no such thing. In order to reach Metal Gear, Snake has to eat Rations to regain his draining health meter while he blinks in eight-bit damage. If you have played Metal Gear Solid 4, this simple gameplay puzzle will likely bring you to tears, for its similarity to the microwave tunnel scene. Only there, Snake can't restore his health with rations.
Also, wince at a line where the Colonel informs Snake that if he refuses to co-operate, he'll be 'in the stockade until [he is] a very old man'. Considering Snake's accelerated aging as a clone and how he looks as of 4, he wouldn't have to be there very long.
In SimCity 2000, if you build your airport too close to your big cities, your planes can and will crash into your skyscrapers, sparking fires and the collapse of said skyscrapers. Yeah. Plane crashes were removed from future installments for obvious reasons.
In the first level of the forgotten NES game Tetrastar: The Fighter, aliens destroy the Statue of Liberty and then go for the World Trade Center, whose destruction the player can prevent.
Rainbow Six: Rogue Spear: Black Thorn originally had the eighth mission set in a airport terminal. After 9/11 it was changed to a bus depot, but the developers actually sent the level designs to modders who wanted to restore the original level.
Rogue Spear itself had Perfect Sword, where terrorists hold an airliner hostage.
The third mission in Silent Scope 2, which came out less than a year before 9/11, has a cargo plane being hijacked, and it crashes at the end of the mission. Worse, the PS2 version was released on 9/11.
In Final Fantasy Tactics, the guy who founded the corrupt church of Glabados, Ajora Glabados, who was also implied to be the Anti Christ or at least under Demonic Possession of the Lucavi Ultima, was born on September 11. His actions in the game alone are bad enough as it is. It gets worse approximately three to four years later, with the real-life 9/11.
And then there's this◊ from The Legend of Zelda: Majora's Mask. A closer depiction to the Die Hard example above. Reads "the end is coming October 26". Majora's Mask released October 26, 2000, which was 1 year, 2 weeks and 2 days prior to the Trade Center attack.
Another case that involved the death of Liam Neeson's wife: the character he voiced for the game Fallout 3 loses his wife in the intro sequence.
One of the missions in Shadow the Hedgehog requires the player to complement a(n alien) terrorist attack by detonating five large bombs planted around a city centre. The game was actually released after the attacks on London, but the mission would have been completed well before.
In 1998, the makers of Doonesbury released Doonesbury Flashbacks: 25 Years of Serious Fun, which contained an archive of every strip published up until that point, as well as numerous extras. Each menu on the disc featured "fun" little animations. The menu for the archive itself was an exterior shot of the White House. One of the many "wacky" things that goes on if the viewer leaves the menu on long enough: an airplane crashing on the White House lawn.
An in-game example comes from Tales Of Symphonia. Close to the beginning, there is a cutscene about Lloyd's Exphere in with Genis says something about his mother protecting him through it. It feels way heavier the second time you play it since you then know that the Desians imprisoned his mother's probably still conscious soul in the stone, which gives it its power.
Modern Warfare 2 was highly controversial at its release for including a level in which the player is part of a terrorist attack on a Moscow airport as an undercover agent. In January 2011, actual terrorists also decided that the airport would make an excellent target. However, they used explosives instead of machine guns (which had been used in a terrorist attack on an airport in India earlier).
An earlier example would be the first Modern Warfare, which was made in 2007, but took place in 2011. Now that the actual year 2011 has rolled around, the events of the Arab Spring, especially the stuff going on in Libya, make the depictions of civil unrest, a violent coup, and subsequent Western intervention across the course of Al-Asad's rise to power seem chillingly prophetic.
And now Anders blowing up the Chantry in Dragon Age II is rather uncomfortable in the wake of the 2011 Norway attacks, especially since the perpetrator happens to share the same name with him.
The Asian-themed level "Tsunami" in Crash Bandicoot The Wrath Of Cortex in which you evade a small tsunami and then explored around the flooded remains. Granted the game's levels were themed around natural disasters, though at this point in time, it's hard not to view it in a rather grim fashion.
In Pokemon Ruby And Sapphire, the player is charged with fighting water- or fire-themed villains. The villains want to use the games' legendary Pokémon to their various ends, but the legendary Pokémon turn out to be too powerful, and end up causing torrential downpours threatening to flood the entire world (in the case of the water Pokémon) or causing massive worldwide droughts, threatening people with starvation (in the case of the fire Pokémon). It all looks like a standard case of Gone Horribly Right, but takes on a new meaning if you consider that some of these things are happening (or threatening to happen) nowadays as a result of global climate change.
Take a look inside the Pewter City Museum in the first-gen Pokemon Red And Blue(and Yellow). Among the displays is a space shuttle, labelled Space Shuttle Columbia. The name is removed in the Gen IV remakes.
The Kanto region also features an abandoned and ruined power plant, in about the same spot where the Tokai Nuclear Power Plant exists in Real Life. Tokai was one of the plants which faced meltdown after the 2011 Earthquake and Tsunami. Since Pokémon is implied to occur in a parallel universe, It makes one wonder where Pokémon reallycamefrom, and how long the ruins have been there...
Though by this logic, it becomes more Heartwarming In Hindsight in the Johto-based games, where said power plant has, within just three years, been renovated and is in use again.
In Pokémon Black 2 and White 2, about half of the Unova region (based on the New York City area and part of New Jersey) is frozen over by a tremendous snowstorm, forcing many characters to relocate and leaving the fates of others uncertain. In 2012, a good chunk of New York City and part of New Jersey was flooded and/or otherwise damaged by Hurricane Sandy, forcing many people to relocate and leaving the fates of others uncertain.
There's a mild in-game example of this: Before you get your first Pokémon, your rival's little sister tells you to make sure you take good care of it. When you reach Nimbasa City, you learn that her Pokémon was stolen five years ago by Team Plasma, and your rival is hell-bent on getting it back and taking revenge on them.
Tron 2.0 and its sequel comic Ghost in the Machine came out in 2003, well before TRON: Legacy was even written. 2.0 is even considered Canon Discontinuity or Alternate Continuity. Still, about half the game's plot straddle the line between this and Hilarious in Hindsight when it comes to light that in both timelines, Tron and Flynn vanished under mysterious circumstances. There was also a plot element with a Tron upgrade code (which is called the Tron Legacy code...) with an unfortunate bug in it that turns the Program it's installed into Ax Crazy.
Even one of the weapons counts. The Sequencer disc allows Jet to split his disc into multiple parts and fight with them. Remember who fights with multiple discs in the canon sequel?
And for more unfortunate moments in TRON games, check out the Intellivision games. Due to Mattel getting an early draft of the script, they screwed up and made Tron an orange (bad guy colored) sprite, cutting through hordes of blue (good guy colored) enemies. A simple mix-up in 1982 gets much nastier when you factor in "Rinzler." The other one is from Maze-A-Tron. You're playing Flynn, trapped on a circuit board and trying to navigate the maze - alone, with no way to win...
One of the most gut-wrenching is this quote from Diego Armando/Godot when he is describing Maggey Byrde's supposed guilt: "Using the dark, aromatic depths of coffee to conceal the poison...classy lady!" It really hits home when you find out Armando himself was poisoned by the murderous Dahila Hathorne and fell into a five-year coma, during which time Mia Fey, the love of his life, was murdered. Poor guy really had in rough...
Another example comes in Rise from the Ashes in the first game. Phoenix be accused of illegally withholding a piece of crucial evidence and having Gant say his badge will be taken away becomes a lot more apparent and foreshadowed when Phoenix is disbarred in the fourth game after he unknowingly presents forged evidence during a murder trial. This could however be a deliberate for foreshadow since Rise from the Ashes was made and released in the DS port for the first time while the fourth game was probably already in development.
Another in-story example from Halo: Reach: Noble Six is notified to be a soldier with a hyper-lethal skill set and a lone wolf personality. Carter, Noble Team's leader and Noble Six's new commander, upon meeting Noble Six tells them that he is happy to have a soldier with Noble Six's skill set on the team but that those lone wolf tendencies should stay behind now that he/she is part of a team. Near the end of the game Noble Team is assigned to defend the Pillar of Autumn and all of Noble Team dies in the process except for Noble Six (and Jun who escaped with Dr. Hasley according to Word Of God) who stays behind on Reach to make sure the Pillar can escape Reach. Carter's statements become sadly ironic as Noble Six is left alone as the only Spartan, or UNSC soldier period, on Reach and all he/she can do is watch as Reach is glassed by the Covenant. Forced to become a lone wolf once again Noble Six's final actions are to fight against unrelenting waves of Covenant forces in a Last Stand that lasts for several hours until he/she is finally subdued and killed. Decades later, the only reminder on Reach that any sort of conflict had ever occurred is the shattered remains of Noble Six's helmet, a lone wolf but a noble and courageous one indeed.
An in story example for Assassins Creed Revelations. On the final mission Ezio goes into the library in Masyaf, there are absolutely no books or anything at all, save a ring of chairs with only one occupant: the skeleton of Altair. You then have an Altair Memory, of him dousing all of the torches in the hall to the library (mirroring Ezio relighting them as he goes into it) and then hiding the Apple of Eden behind a wall. The final mission statement? Take a seat and rest for a bit.
Comes again in Assassins Creed Brotherhood, when you realize that he had lost another loved one in the city he lived in and watched helplessly as his father and brothers were executed. He had every reason to brutally execute Savonarola for the death of Cristina. It took a lot of self control to not give him the same fate he had given Vieri and Uberto
In Ghost Recon, released in 2002 and set in 2008, a war between NATO and an Ultranationalist Russia starts off with the Russians backing Georgian separatists in an invasion of Georgia. Fast forward to 2008 and...
In Mass Effect 1, Ashley writes an e-mail to her sister warning her not to fraternize, as she doesn't want to have romantic feelings come into play when deciding which of her subordinates lives or who dies. On Virmire, where you must choose between saving Kaidan and Ashley, both of whom can be romanced, it's possible to sacrifice Ashley to save a romanced Kaidan or save a romanced Ashley at the cost of Kaidan's life, making Ashley a potential victim or reluctant beneficiary of this kind of thought.
In Mass Effect 3, if you choose to allow the quarians to destroy the geth, EDI will criticize the logic behind your decision, suggesting that if given the choice, Shepard would save Joker over her. This gets even harsher if, at the end of the game, you take the Destroy ending, which not only destroys the Reapers, but all synthetic life in the galaxy, EDI included.
Zaeed Massani can die on several occasions in Mass Effect 2 or 3, but those scenes started hitting much harder after his voice actor Robin Sachs died (shortly before the release of the last downloadable chapter featuring Zaeed).
An in-game (and fully intended) example in Diablo III: During Act 3, Leah's journal mentions how the spirits she's trying to keep trapped within the black soulstone are starting to wear on her, but comforts herself by remembering that once Asmodan is dead and captured, and the black soulstone is destroyed, she'll be herself again. At the end of the act, before the soulstone can be destroyed, Diablo's spirit is freed from the stone and placed into Leah's body, turning her into the Prime Evil and the end boss of the game, whom the player must then destroy to save the day.
An in-story example occurs in Hatoful Boyfriend. At one point during Nageki's route, Hiyoko tells him (in a non-malicious way) that he's like a friendly ghost that hangs around the library. Then later on it's revealed that Nageki reallyisa ghost (having committed suicide 5 years ago), and is unable to leave the library.
Stalin's death by poison at the end of the Soviet campaign of Command & Conquer: Red Alert. The fact that he was actually poisoned in Real Life which caused his stroke was not known when the game was made.
Spec Ops The Line - released in late June 2012 - is about an unlikely massive Sandstorm that hits Dubai, causing a serious natural disaster. In late October of 2012, Hurricane Sandy hits an unlikely part of the United States in the northern east coast - mainly damaging New Jersey and New York - causing a real natural disaster. Many parts of New Jersey was even reported buried in sand.
Kingdom Hearts 3D makes the original Organisation XIII arc much harsher as it reveals that the members were actually growing new hearts. It makes you feel sad for Demyx, "Oh, we do too have hearts!".
In Virtues Last Reward, Quark gives Sigma a letter about how he met his adoptive grandfather and how he gushed about getting a chance to have root beer float which none of his friends ever had. This is actually a hint that the world has been fucked.
Knights of the Old Republic has a bucketful if you've played Star Wars: The Old Republic. That Hope Spot (and lightside boost) on Taris with those Outcasts? Yeah, instead of a quick death by orbital bombardment, you instead condemned the lot to be picked off by disease, rakghouls, starvation, and finished off with toxic waste. Playing the "canonical" option as a Light Side Male with a Bastila romance? Well, your character knocks Bastila up, has a Force vision about the Humanoid Abomination Sith Emperor, and runs off to try and stop it, leaving their friends and loved ones behind without so much as a holocron warning them about the threat or telling them why you had to leave. They spend the rest of their lives waiting and you never return. Even worse is if you go canon with the sequel, which is already running on this Trope. Exile hooks up with Revan, they try to take on the Emperor. Lord Scourge literally stabs Exile in the back, Revan ends up with the same fate Malak put all those Jedi in, then goes insane and tries to commit genocide of anyone with a trace of Sith blood before the Imperials save the galaxy by putting him out of his misery. Canderous's people become vassles of the Sith again (whith those who followed his teachings hunted down by the Imperials), and the Sith charge in and lay waste to half the Republic anyway - so everything in both games turned out to be near-completely pointless.
In Earthbound, Ness can randomly get Homesickness, a crippling condition which causes him to waste turns in battle thinking about home. The only way to cure it is by calling Mom. Good thing this doesn't happen to Lucas in Mother 3!
Pretty much everything involving Penelope in Sly 3 becomes really painful after knowing she does a Face Heel Turn in the fourth game.
Minesweeper has an option to change from defusing mines to avoid flowers because people who play the game also happen to be victims of landmines.