For a long time, video game protagonists either relied on dodging if they were One Hit Point Wonders, or simply soaked up the damage if they were Made of Iron. Taking cover was certainly possible, but it simply consisted of stepping behind walls.
In recent years, cover and systems for using it effectively have become automated to an extent. The first examples of formalization like this in First and Third Person Shooters were “duck,” “lean left” and “lean right” keys present for quick peeks and potshots, often inherited from Stealth Games. In the newest titles, pressing a button causes your character to press up against nearby objects, sidle left and right along them, and peek around corners. With another button, one can either fire blindly, or expose oneself to rapidly aim and shoot. A third person shooter with a cover system is a member of the relatively new “cover-based shooter” sub-genre.
Many cover systems exaggerate the safety of cover by allowing the player to see around corners the character can't (some first person games even jump to a 3rd-person camera when sidling against cover for this reason,) allowing them to pre-aim or designate targets from behind cover, rendering them invisible to enemies while they lean around corners, or even letting them fire aimed shots from behind cover. In essence, this is an inversion of Behind the Black.
Games based on this trope are pretty much guaranteed to be full of waist-high obstacles to duck behind, no matter what environment you're in. And they're all inexplicably bulletproof.
In a strategy game, Geo Effects might provide a defensive bonus for units in cover, or Garrisonable Structures for infantry to use as cover. See also Corridor Cubbyhole Run, a favorite level design choice for a cover-based shooter; and Die, Chair! Die! for destructible objects, which might be good cover exactly once. And please, don't try to take cover behind the random barrels of explosives. Using a person as cover is its own trope.
While not a new concept (as certain games are made so tough you want to find a barrier between you and your enemy even if you don't have a formalized cover system), the wild success of Gears of War has lead to its recent replication in a long series of what are effectively Follow the Leader games. It's basically RPG Elements for a new era of gaming, and a reflection of changing tastes.
Rainbow Six games have had peeking around corners since the first game (like in Metal Gear Solid), but Vegas added the "jump to third person" type, where the player can shoot around the corner (like in Metal Gear Solid 2) and blind fire (like in Kill Switch). Vegas 2 also had a cover penetration system like Modern Warfare and World at War, along with shields that could be used to protect yourself while on the move, at the cost of taking one of your weapon slots.
The main concept behind Full Spectrum Warrior is to advance your squads from cover to cover, making them (and enemies) impervious to bullets from certain angles. Since this is a tactical game and not a shooter, your soldiers will complain loudly if they're dangerously exposed, and there's a key that'll—in theory—have them scramble to the nearest cover quickly.
The World War II squad-based shooterBrothers in Arms: Hell's Highway introduced a cover system to the series, apparently based on Rainbow Six Vegas. Proper use of cover, suppressing fire, and flanking is a key focus of the series. For some reason, just crouching doesn't get low enough and leaves your head exposed, meaning you have to use the third-person cover system unless you want to get shot.
Call of Juarez: Bound in Blood has a rather nicely executed version. Walk up to, say, a crate, and your character will automatically crouch just low enough so that they can shoot over it, while exposing himself to as little incoming fire as possible, at which point you can press the crouch button to get completely behind cover. He will also lean around corners automatically, though this doesn't work as well.
Perfect Dark Zero has an "aim from behind cover, pop out and shoot" system similar to third-person shooters.
Red Orchestra 2 does this more realistically than most. Cover doesn't consist of a convenient series of waist-high barriers; one's head could be exposed, and blind-firing over cover is actually blind.
You can crouch to take cover in Battlefield: Bad Company 1 & 2, but since the game awesomely averts the Insurmountable Waist High Fence trope by allowing players to blow up and destroy most of the game's environment (which includes buildings), you better hope no one spots you.
Crysis 2 introduced a subtle example. When the player is ducking behind low cover, or standing near the convex corner of a wall, attempting to aim down the weapon's sights while looking at the edge of the cover will make the Player Character lean over or out of the cover to take shots while only exposing a portion of their profile. The player never "sticks" to the cover, which tends to make the system a little less obvious than many other examples.
F.E.A.R. 3 uses a system similar to the one from Crysis, although the player does press a button to stick to cover and can emerge to fire, which is referred to as "active cover".
GoldenEye Wii doesn't have an explicit cover system but if you're behind a solid object, aiming down the sights will have Bond stand up to see over the obstruction to return fire.
Kill.Switch (2003) by Namco can be credited for being Trope Codifier and Trope Namer of the whole "Third-Person Shooter Cover System"™ gameplay mechanic. However, despite being a good game and a multi-platform release, it wasn't a massive blockbuster hit and only a modest number of people remember it as the pioneer of the third-person shooter cover system. Of course, one of those people was Cliffy B. And despite him giving the game credit at every opportunity, it's still obscure.
Win Back (1999) came out four years (two if you only know about the PS2 port) before Kill.Switch featuring a similar cover system, but lacking the blind-fire and move-and-shoot elements of Kill.Switch.
Metal Gear Solid (1998) featured a peek-around-the-corner cover mechanic, where Solid Snake can press against walls and peek around corners.
Metal Gear Solid 2 (2001) expanded on its predecessor's cover mechanic, introducing a shoot-around-the-corner cover system, where Snake or Raiden can press against walls and aim from behind them, to shoot from around the corner of a wall. This shoot-around-the-corner cover system has also been employed in later games featuring Stealth, like the Splinter Cell series, Everything or Nothing (2004), and Tactical Shooters like Rainbow Six Vegas (2006).
Metal Gear Solid 4 features an improved cover system that is more similar to the Kill Switch cover system.
Resident Evil 4 (2005), developed by Shinji Mikami at Capcom, featured a cover mechanic at a few scripted instances of the game, in places where enemies pack heavy firepower. The game also introduced the Over The Shoulder perspective now common in third-person cover shooters.
Resident Evil 5 features an improved cover mechanic in its gameplay, but like its predecessor, you only get to use it during a couple of scripted instances. Incidentally, it becomes available after you start encountering enemies that pack heavy firepower.
While cover systems have existed before it, the popularizer of cover in Third-Person Shooter games is Gears of War (2006). Zero Punctuation made light of this, as it seems all the bombs used in this period are designed to leave the walls of ruined buildings standing at exactly waist height.
Uncharted: Drake's Fortune utilizes an impressive cover system - duck behind chest-high wall, lean from behind tree, hang from cliff and chin up to shoot. The game's cover mechanic was demonstrated at E3 2006, months before the release of Gears Of War. Like Cliffy B, the creators of Uncharted have cited Kill.Switch as inspiration for its cover system.
Made even better in the second one, Uncharted 2 Among Thieves. You haven't lived until you've pulled an enemy off the cliff you're hanging from, or, even better, doing a 300 style kick to knock enemy's out of their hanging cover to their deaths. Tends to elicit curses in online matches.
Cover is the main mechanic of Eat Lead: The Return of Matt Hazard, it has a cover to cover system that makes Matt automatically run from place to place at the press of a button.
Terminator Salvation uses a very similar system, which is invaluable given the enemies' usual tactics. You spend quite a lot of time in the game pinned behind some abandoned car or waist-high wall by minigun fire.
Grand Theft Auto IV almost exactly copied Gears Of War's system. One can use his own any vehicle as cover, a tactic used in real life by police, but since damaged cars can explode, don't count on it lasting forever.
Ghost Hunter had a cover system. In first person mode Lazarus could lean out from cover and shoot with almost no risk to himself.
The John Woo game Stranglehold is a Third-Person Shooter that has Tequila taking cover from time to time, planting his back to a wall, column or other piece of cover and leaning to the side to blast away. This, along with Bullet Time and Leap and Fire tactics, is one of the keys to making it through the game, and is absolutely essential for survival on later stages, which have bad guys subjecting you to very, very, very heavy fire. And considering one of Stranglehold's main conceits is "Massive Destructibility," cover never lasts very long.
Vanquish, developed by Shinji Mikami and published by Sega, is a unique variation. While cover exists, you're quite a bit more robust than most cover-using protagonists, and have a number of high-speed moves that allow you to easily dodge enemy fire while retaliating. When you're dangerously low on health, Bullet Time kicks in, allowing you find the necessary chest-high walls easily. The score system also penalizes you based on how long you've spent your time in cover.
They are using this (along with many other Third-Person Shooter concepts) in a Harry Potter: The Deathly Hallows, of all things. "Ron! Confringo those death eaters! Oscar Mike!"
Enslaved: Odyssey to the West is not, strictly speaking, a shooter, but it does have a cover system. Monkey's ranged attack is awkward and has a low ammo count, so firing from cover is not practical most of the time. Rather, Monkey and Trip tend to take turns drawing fire and advancing under fire, so Monkey can close to melee range.
In the DLC campaign, Pigsy is a ranged fighter so he plays it much straighter, and uses his grenades, traps and rifle from cover.
Batman: Arkham Asylum and its sequel use a limited cover system, but Batman doesn't shoot. Rather, he can throw batarangs (and a few other gadgets) and ambush patrolling goons from cover positions.
The first two Max Payne titles didn't have a cover system but the third game does let you duck behind cover.
Similar to Metal Gear Solid Headhunter focused on sneaking around areas by hugging the wall until the right time to strike.
The Syphon Filter series, unfortunately, had to wait until the fifth game for a proper snap-to-cover system.
Infantry in End War need cover or buildings to garrison to survive in combat. In fact, engineers are specifically stated to be good against all vehicles in the game, but only if they're in cover or a building while fighting vehicles.
Company of Heroes has an extensive cover system for its infantry units. The hard counter is, as in real life, grenades, flamethrowers, mortars and flanking.
Warhammer 40,000: Dawn of War II, from the same studio, is much the same. The additional counters in this case are the assault unit, melee-focused soldiers that can charge the enemy via teleportation, jetpacks, or just utilizing Attack! Attack! Attack! and cut them to pieces with melee weapons (like Chainswords), or smashing that cover with heavier units, frequently vehicles. Vehicles can be used in cover also!
The first Dawn of War also had a cover system and assault units were also the great counter. That or just dropping an artillery shell on top of the cowering squad, which frequently blows them out of cover.
For that matter, cover is supremely important in the tabletop version of Warhammer 40K, especially for units with poor armour like Imperial Guardsmen.
Cover is very important in the old X-Com games since even the best soldiers in the best armour can be taken out in one shot. Grenades, bigger bombs, and powerful weapons can all be used to destroy cover and each terrain object has a number of 'hit points' that indicates how sturdy it is.
Cover is also very important when avoiding explosive weaponry. Because of the way explosions are handled, a blast will destroy a wall or object, but if someone is hiding behind the wall or object, it'll still stop the blast. This is why doubling up on firing rockets or using the autocannon's high explosive rounds in burst mode is highly recommended for hunting out aliens in cover. One rocket or shell destroys the cover, the others get the alien lurking behind the wall.
In the 2012 remake XCOM: Enemy Unknown cover specifically makes targets harder to hit, with terrain features providing either half or full cover against enemy fire. Snipers can take a perk to double the amount of cover they get, and gunfire that misses units in cover may instead hit the cover and destroy it. Rockets are useful for destroying both the cover and units behind it.
Another Spiritual Successor of the game, Xenonauts, features more sophisticated cover mechanics than the original, as the AI loves kneeling behind boulders and other low cover (and shooting).
Emperor: Battle for Dune introduced dedicated areas of "infantry rock" where infantry could take cover and be safe either from sandworm attacks or being run over by enemy vehicles (this probably being a balancing decision as otherwise infantry would be too underpowered).
Strictly speaking infantry rock was around in previous games — it's just that because their effects were limited to being impassable to vehicles, they didn't fall under this trope (the 'safe from being run over' thing still applies, of course).
Infantry units in World in Conflict could take cover within buildings and forests. The former rendered them immune to all damage—until the building was leveled by enemy fire and everyone still inside died. The latter gave them a small defense bonus, protected them from being run over, and rendered them invisible to all non-infantry unit as long as they didn't shoot. That last ability gave rise to the strategy where Anti-Air players drop paratroopers into forest near enemy positions and have them passively provide targeting data for the less mobile and shorter-sighted but hard hitting units.
Cabal for the arcade had destructible terrain that you could take cover behind from enemy shots. Of course, those damn helicopters would blow your cover away and still hit you.
Blood Brothers, the spiritual sequel, was much the same, though there are entire levels with zero cover.
The Time CrisisLight Gun Games use a cover mechanic, operated by a foot pedal on the arcade machines. Ducking into cover is also the reload method. The game's cover mechanic predates all of the shooters mentioned above, though its creator Namco was later responsible for Kill.Switch.
The Police 911 series is an expansion of this idea, using motion sensors instead of a foot pedal. The first game got ported to the PS2. Guess how that went.
Star Wars: The Old Republic is the first Massively Multi-player Online Role Playing Game to feature a full cover system. It's used exclusively by the Smuggler and Imperial Agent classes, and several of their abilities can ONLY be used if they are behind cover.
It's an interesting example, as well: once the Agent and Smuggler reach level ten and gain their advanced classes, their cover ability creates a red or blue respectivelyBeehive Barrier for them to hide behind if no other cover is available. It provides a slightly smaller cone of cover than many of the world objects players can take advantage of, so it's for use as a last resort or if none of said objects are in the area. Boss areas, even if they're not obviously so to begin with and especially those tailored for the cover classes (i.e., those in their story areas), usually have plenty of cover available.
The 2002 remake Space Raiders used a similar type of cover mechanic, where the player's character can take cover behind destructible objects.
The Rolling Thunder games were the first Run & Gun and Side-Scrolling games to feature a cover mechanic. They were developed by Namco, who later created the pioneeering cover shooters Time Crisis and Kill.Switch.
Mass Effect 1 included a cover system where you would automatically stick to walls/waist high crates that you got close to. It was generally effective but could be annoying if you didn't want to take cover and the game decided you did. Fortunately once your powers evolved far enough you didn't need to use it.
Mass Effect 2 improved this mechanic by having a get into/out of cover button. Unfortunately, at least on the Xbox 360 it's mapped to the same button as "run" and nothing cuts down your life expectancy quite like getting stuck to a wall when you try to run away from a charging krogan... Even better: jumping over the cover you were trying to get behind. The run/get-into-cover/get-out-of-cover button is also the vault-over-obstacle button. That said, when it did work, having the same button do all three things could have some awesome effects, like having Shepard sprint towards cover and slide the last five or ten feet like a baseball player. It depended partially on player reflexes and largely on the layout of the room.
Also, unlike the first game, where you could ignore cover once you got powerful enough, without being in cover in the sequels you will die very very quickly.
With exception of the Vanguard class, the only class in the series who doesn't need to use cover at all. Due to the fact that their combat is based around charging straight at enemies and engaging in point-blank range.
PC players have it much easier given that a mouse and keyboard has a lot more available buttons than the typical controller. "Take Cover" is your "Use object" key, "vault cover" is "use"+"walk forward", and sprint is its own key entirely.
Mass Effect 3 finally got the formula balanced right, and its gameplay is typically heralded as the apex of the franchise. What's a bit ironic is that all three Mass Effect games not only came out after Gears had successfully codified the trope, but use the same Game Engine (the one belonging to Unreal Tournament 3) that Gears did.
Speaking of waist-high cover being everywhere, the Mass Effect games seem to treat jersey barriers the way other games treat wooden crates. This is used to mess with the player's expectations on at least one mission in a massive spaceship where these waist-high barriers are everywhere, but enemies are nowhere to be found for the first ten or fifteen minutes.
Pretty much every modern pen & paper RPG has rules for making use of cover.
In World of Tanks, buildings and other terrain features can be used to block enemy fire, though artillery can bypass some of it from the right angle. Some buildings can also be destroyed by shooting or running over them.
The trailers in Serious Sam 3: BFE make fun of taking cover mechanic. The game's slogan is also "No cover, all man!"
Warhammer 40,000: Space Marine gets in on this as well, and their tagline is intended as a deliberate Take That against Gears of War: "Cover is for the weak!" (This is probably also a sly reference to the fact that, in the tabletop game, Space Marines rarely gain any advantage for being in cover. The save it provides is worse than their armor save, and you can only use one save against any attack.) Though there are times when it is advisable to take cover at least long enough for your armor to regenerate.