The Dev Team Thinks of Everything/Metal Gear

Metal Gear Solid / Twin Snakes

 * Psycho Mantis can read the player's mind by reading memory card data, providing a detailed analysis of the player's proficiency at the game (how good they are at stealth and combat, and how frequently they've saved their game), and suggesting that the player enjoys certain games like, say, Castlevania, for instance, or Super Mario Sunshine and Super Smash Bros. Melee in the Gamecube port. Even better, in the japanese version, having save data from both Snatcher and Policenauts unlocks a special message from Hideo Kojima.
 * If you don't take the SOCOM pistol from the truck in the heliport, the cutscene when Meryl lets you out of the cell will be different. Snake will push aside the barrel of her gun instead of aiming back at her.
 * If you attack Meryl when she's following you, she'll slap you and knock you down normally, although if you hide in a box afterwards, she can't hit you back. However, if you do this in an area with wolfdogs that are friendly to her, she'll instead whistle and cause one of them to pee on your box, and wearing that same box afterwards will cause the wolfdogs to ignore you due to the scent.
 * Having Sniper Wolf's handkerchief equipped will cause the wolfdogs to follow you without attacking and it doesn't require any additional gimmickry from player's part, but once Snake, you obviously can't use it anymore and need to resort to the box trick described above.
 * One of the most famous things in the original MGS was the box warp. By climbing onto a supplies vehicle and equipping a box from elsewhere in the game, you could be transported to that location.
 * If the player is fighting the Hind with the Mono sound setting on, an optional codec call can be accessed where Roy Campbell expresses disappointment that Snake doesn't have Stereo, or Naomi stating that Snake isn't any less of a man for using mono.
 * In the fight with the Cyborg Ninja, he makes a big scene out of the fact that you can fight hand-to-hand. Indeed, most of your weapons are useless. You can, however, freeze him for a few seconds using a Chaff Grenade. If you do, not only can he criticise Snake for not being what he was, he can also break the rules himself and use his sword.
 * On the way to the fight with Vulcan Raven, you can kill the birds you see. If you do, Vulcan Raven is pissed when you encounter him.
 * Depending on the player's decisions, Snake can either enter the top ventilation shaft to first infiltrate the Tank hangar building or the bottom ventilation shaft. The decision will be reflected with Miller's introductory call, where, if the bottom shaft is chosen, he will explain to Snake about the rodents that Snake is currently following.
 * Depending on how successfully the Player escapes regarding the ketchup bottle or not, the programmers had Snake's response when the player calls Otacon be different regarding the results: If the player fails to escape via ketchup bottle (either due to not using it at all, or the player wasn't quick in escaping), Snake will coldly refuse to acknowledge Otacon's involvement in the escape. If the player succeeds in escaping via ketchup bottle, Snake will express some surprise that the trick actually worked.

MGS2

 * You can make Snake and Raiden... pleasure themselves to the bikini posters scattered throughout the game (and have people on the other end of the codec comment on it [and have your character comment on their comments]), get your codec support mad at you for punching hostages or photographing the panties of female hostages, destroy a huge amount of inanimate objects for the time, and get comments from Snake referencing things you won't find out he did until much later during Raiden's story if you call him at the right times.
 * There's a bucket of ice in the crew's lounge on the Tanker. If you shoot it, not only does the ice fly out, it melts realistically; the cubes closer to one another melt slower than the isolated ones.
 * Also, those Ketchup bottles onboard the Tanker and Strut C of Big Shell? You can shoot at them and cause them to explode, also distracting enemies that way.
 * There are seagulls on the Big Shell, and killing enough birds as Raiden gets a call from the Colonel and Rose, who chew you out of animal cruelty. Rose will break up with you and won't let you save until you apologize. Same goes for hitting hostages.
 * If you enter the only place with a mirror on the Big Shell and equip either the Camera or Sniper Rifle (weapons that force you into first person mode and which you won't have the first time you visit), you see that Raiden is properly rendered holding either.
 * There's a point in the game where Raiden is discovered regardless of how good you are, and the whole facility goes onto high alert. If you return (with no purpose in the storyline) to some of the earlier parts of the facility at this point, there are more guards. This is also the only way to get some of the dog tags.
 * In the Tanker chapter, you get a camera which is important to the mission, but can be used anywhere. It's not surprising that players might try to take photos of things which aren't important to the mission, and photographing posters, hidden characters and female soldiers gets you secret replies from Otacon.
 * The box warp returns in the form of a parcel sorting system.
 * There are two ways you can get a 'Mission Failed' which are highly unlikely in normal gameplay: falling down the lift shaft on Strut A and letting the bomb explode after the battle with Fatman. Both of these have their own specially-created images for the game over screen.
 * The game takes into account the fact that certain bosses can be defeated in different ways. The cutscene after the Olga fight varies depending on where she was when you shot her, and Fatman is visibly still alive and breathing after the fight if you take him out with a non-lethal weapon.
 * At one point in the game, you have to find a hostage by calling out to them, with a button command that stops working after the hostage is found. If you then backtrack to the room with a parrot in it, and call out to the parrot enough times (ten or eleven. With no indication that what you're doing is recognised by the game), it learns to say the phrase and adds it into its usual repertoire.
 * The parrot can also learn to say "Enemy sighted, requesting backup" if you get caught too much in that area.
 * When the player sees a cardboard box in the Strut connection area early in the game, he or she might decide to shoot it and cause the occupant to retreat quickly. This is later reflected in a codec call about the box, with Pliskin irritably telling Raiden that thanks to him, a couple of his boxes were destroyed before stopping himself, should the player decide to do that.
 * Plant some C4 in front of sea lice and blow them up while in first person mode: The sea lice will then fly towards the "camera" and splatter against it in a manner similar to insects on windshields of a speeding car.
 * The player might get the idea to hack the escape from Arsenal Gear's torture room regarding Raiden's... lack of clothing. The developers apparently anticipated this and made absolute sure they didn't model that area, although lines by the guards still imply the presence and the actual size of his manhood.

MGS3

 * We're talking about a game series that accounted for the possibility of the player shooting guards in the crotch, and incorporated it into that bit with the Sorrow in MGS3. "I'm useless now!"
 * We're talking about a series that also accounted for the possibility that the player might have eaten a vulture who had, in turn, eaten human flesh. The victims of Snake's cannibalism-by-proxy also appear in the Sorrow's river, complete with a vulture on their shoulder. ("You ate me!")
 * You can also find a crocodile cap and peek around corners while crawling, causing guards to believe you are some kind of indoor crocodile and freak out.
 * Similarly, you might try to use it on the dogs to see their reaction: The dogs will turn tail and flee if you do so.
 * If Snake gets a stomach ache from eating rotten food, you can cure him with medicine OR go to the medical screen, spin him around a dozen times, and then exit the screen and watch Snake puke up, fixing the problem.
 * It's possible to kill The End just after the cutscene in which he's fully introduced. If you do so, the boss battle is replaced by an encounter with the Ocelot Unit.
 * You can also save during The End's boss battle, and leave the console off for a week. This results in him dying of old age.
 * Calling your Mission Control when you're imprisoned, saving and then loading the game causes Snake to have a nightmare, which manifests itself as a demo for a scrapped action game called Guy Savage.
 * During the short period of time you have Eva in your party, so to speak, you can check her medical history. Turns out she has breast implants, she has eaten a Tsuchinoko, and Proctitis. Is it possible for Kojima to troll his own series?
 * This can be seen as Fridge Horror, if you consider that the proctitis is usually in the midst of electrical burns and other wounds caused by the sadistic pervert Depraved Bisexual Big Bad. Yep.
 * Better yet, if you tranquilize her (which significantly slows down her stamina drain), she'll start talking in her sleep about Snake, The Boss and her dog, and makes several sexually suggestive double entendres.
 * If you harass Eva enough times while you're paired up with her, she kicks you in the crotch hard enough to cause an instakill and a Game Over.
 * There is a Codec conversation for an absurd amount of elements in the game.
 * You know the torch you find in the cave? You can use it to set foes on fire.
 * Also, you might get the idea to use the torch in Groznyj Grad's Underground Tunnel up to arriving at the area to face The Fury. The programmers anticipated this possibility, and added in a few seconds to The Fury's debut cutscene that shows Snake dropping the Torch just for that specific scenario.
 * Shoot or stab Ocelot anywhere on the body without killing him. He will possess a bandage in that spot in all future appearances.
 * There's a moment during the Virtuous Mission where Ocelot is knocked out on the ground. If you kill Ocelot while he's out cold, you get a Game Over with Colonel Campbell telling you that you created a time paradox, and that you shouldn't screw around with the future. The HD re-release even has an achievement called "Problem Solved, Series Over" for doing it.
 * If you backtrack to areas you previously visited and called EVA there (more specifically in areas such as Dremuchij, Dolinovodno, Ponizovje, and Graniny Gorki, the four places where you can't call EVA upon the first visit due to either being absent [Ponizovje and Graniny Gorki], or hadn't even met yet [Dremuchij and Dolinovodno]), in addition to giving Snake the info about the location he is currently at, EVA will also ask Snake what he's doing all the way back there and remind him that he was supposed to go to the next destination.
 * Various Codec calls and conversations to characters will also be slightly different depending on the player's prior actions. In Rassvet, for example, Snake's response to Zero in regards to the guard level depends on how the player handles sneaking past the guards. If the player evades detection completely, Snake will respond with "No one spotted me." Likewise, if he gets an alert or kills the soldiers, he'll respond with "I managed to get past them." and "I had to kill them... there was no other way. But no one will know we were involved." Also, call Sigint when the flame troops arrive at Krasnogorje. If the player got a bit too triggerhappy with soldiers, Sigint will state that the reason why they are after Snake is because he killed many of their comrades. Likewise, if the player restrained him/herself from killing anyone (except for maybe the Cobra Unit), Sigint will respond with Volgin sending them to torch him as revenge for disposing of The Pain, The Fear, and The End. In addition, Volgin's analysis on his body check on Snake before torturing him will be different depending on how frequent the player seriously injured him/herself gameplay-wise. If the player had very little, if any, (serious) injuries prior to being tortured, Volgin will state "What a beautiful body you have, like a newborn baby. But not for long..." If the player received a moderate amount of injuries, Volgin will state "Hmm... you've certainly seen your share of battles. Consider yourself lucky. I am about to show you what hell is really like." Lastly, if the player received a lot of injuries, Volgin will say "You're a tough one my friend, a lesser man would be dead by now."
 * If the player still had the magazine in their possession up to their capture, and then the player calls EVA upon leaving the prison, EVA will mention that she did not throw out any of Snake's equipment, and also reveal that she found out about the magazine, while sarcastically referring to it as a "fine piece of literature" towards an embarrassed Snake.

MGS4

 * You can unlock, with some difficulty, the Solar Gun from Boktai. It's very powerful, but difficult and impractical to use due to its limited ammo capacity and the fact that you can only recharge it manually in sunlight. Sunlight, of course, is a stock vampire weakness and the Solar Gun in Boktai kills vampires, so naturally, a player might consider using it on Vamp. He has a special animation and response to the shot (which is almost impossible to land due to how insanely fast he is), and fully-charged it can knock him down him in a single hit.
 * Similar to Metal Gear Solid 3: Snake Eater, spinning Snake around on the model viewer/OctoCamo selection screen will result in Snake vomiting.
 * Have Snake die in various ways, continue, and then call Rosemary. Snake (or, in the event that Snake was killed via an explosion, Rosemary) will begin the call stating that he got the feeling that he was killed before in the specific manner in which the player died.
 * Certain locations in which you can participate in battles between Liquid's PMC forces and local militia change according to how the battle is resolved. You'd usually only spot this by backtracking.

Peace Walker

 * There's a couple of joke Dating Sim missions where you can date either Paz or Kaz. Normally, the game prohibits you from taking weapons into the dates, but if you hack the game to allow you to take them, you can kill them. When Kaz fades, his glasses remain and clatter onto the sand.
 * While the Codec lines in Peace Walker are usually generic or generic for the stage, thus making them hardly worth bothering with for the majority of players, making Big Boss stand on a specific riverbank in a specific stage after recruitment of Huey, the man who will become Otacon's father, leads him to remark that he always gets a bad feeling when he looks out at the water. (Metal Gear Solid 2: Sons of Liberty revealed that Otacon's father committed suicide by drowning himself.)
 * If the player shoots the soldiers in the butt, it will instantly knock them out.
 * The game has two situations prepared depending on how well the CQC quick action cutscene turned out for the player: If the player successfully managed to do the CQC, the player will be able to use the ID card that Snake stole from Strangelove earlier to escape from the cell, although the call with Miller after Snake escapes will be somewhat short. If the player fails, the player can utilize a jigsaw strapped onto him, and after escaping, Miller's codec call will have him reference the Jigsaw.
 * Given the Sling Post's obvious resemblance to a club or baseball bat, the player might get the idea to smash it into enemies. The game programmed it for that specific purpose, and doing so will also activate a codec call where Miller will commment that it's not what its supposed to be used for.

Multiple Games

 * Try shooting the ! above a guard's head if you're discovered. It stuns them momentarily.