The Metal Gear series commonly features an Exclamation Point ("!") over an enemy's head to show that either they have discovered the player and are going to attack, or that the enemy has been distracted by a noise or something else nearby. In the event that an exclamation point appears, the player is able to become aware of a danger and quickly hide, move from the area in which the designated sentry has become interested, or to equip a disguise or the cardboard box.
In the original Metal Gear, a white shock bubble with an exclamation point meant that only the guard team in that area would give chase in an attempt to finish off Snake. In other areas, the shock bubble was colored yellow and there would be two exclamation points inside of it. In this alert phase, enemies across different areas would be alerted and back-up would pour in from off-screen. The only methods that can be used to end this phase are by killing all of the oncoming enemies, moving to a different floor, entering a boss fight area, or entering/exiting a building.
In Metal Gear 2: Solid Snake, the exclamation appears in a small white bubble but the concept of a full red alert is first realized, as Snake cannot disappear to the next screen or simply kill off the backup that comes his way. Instead, he must hide or stay out of sight until the evasion phase finishes.
Beginning in Metal Gear Solid, the actual exclamation mark is depicted as a large, red "!" floating above an enemy upon their discovery of the opposition. Accompanying this symbol are the eyes of vigilant guards flashing with shock.
During the boss fight against Colonel Volgin in Metal Gear Solid 3: Snake Eater, a colorless "!" will appear above Colonel Volgin after being attacked by the player wearing the Raikov mask, shortly before rushing angrily at the player. However, the sound effect will not play.
In Metal Gear Solid 4: Guns of the Patriots, when Snake first encounters Jonathan from the Rat Patrol, Jonathan's haircut, when seen from behind, looks like an exclamation point and the trademark sound effect is played. In a subtle reference to this, Meryl also tells Snake that sneaking up on him from behind is a very bad idea.
The exclamation point is not the only piece of punctuation that appears above the opposition in the Metal Gear series. Whilst a colorless "!" means that the enemy has been alerted to a nearby presence through sound or movement, a colorless "?" is evidence that the enemy is curious or confused and will immediately resume his patrols. Actions such as placing distracting devices, such as empty magazines or books, upon the ground route of sentries will cause this behavior. Snake also displays a colorless "?" in a cutscene in Metal Gear Solid while attempting to call the elevator in the Communications Towers.
In Metal Gear Rising: Revengeance, the exclamation point reappears under the same purpose, although the colorless variety was changed to yellow. In addition, it was also slightly redesigned so the vertical line portion is shaped in a similar manner to a lightning bolt, as a brief reference to the meaning of Raiden's name. Also, the exclamation point shows the phase status being placed in it with red being placed as ALERT and yellow being placed as CAUTION. On top of that, the sound effect plays on both of these phases.
The Exclamation Point was originally planned to be dropped from Metal Gear Solid V: Ground Zeroes and Metal Gear Solid V: The Phantom Pain, although it was retained. Also, the box art of The Phantom Pain shows the V in the style of the trademark exclamation point. The exclamation point is also one of the emblems in this game. 
In addition, the exclamation point itself can also mean other things besides discovery of an enemy depending on the circumstance. For example, the exclamation point can appear if the enemy discovers something that acted as a distraction, such as a magazine placed by the player.
Other symbols can also appear over a sentry or an NPC. For example, white, floating Zs will trail off a character who is sleeping and small, yellow stars will circle a character who has been knocked out. A pink heart will also hang over a character if Snake gains a character's trust.
Shooting directly at the exclamation mark above enemy sentries will daze them for a few moments, indicated by white bubbles above the enemy's head.
In Super Smash Bros. Brawl
The exclamation point is such an iconic part of the Metal Gear series that the symbol has appeared in Super Smash Bros. Brawl, alongside the cardboard box, Solid Snake, Otacon, the Codec, Mei Ling, Roy Campbell, Shadow Moses Island, and other famous elements of the Metal Gear series. It is displayed during the Shadow Moses stage whenever the searchlights discover one of the fighters, accompanied by the trademark sound effect. The punctuation mark is also displayed on Snake's cardboard box in-game. The exclamation mark also appears, along with the trademark sound effect, in the Subspace Emissary when Snake is discovered by Lucario. Both uses, however, are completely the opposite of the mark's normal usage in the Metal Gear series, since Snake / other characters have an exclamation point when they are spotted as opposed to an enemy having an exclamation point when they see Snake.
In the Bunnies Can't Infiltrate Games Conventions trailer for Rayman: Raving Rabbids, the convention guard makes the famous alert sound when he spots the Rabbids hiding in a cardboard box.
In the Snake Eyes trailer for Battlefield: Bad Company, when Sweetwater mentions seeing a guy in an eyepatch hiding in a drum can, an ! appears over the drum can before Haggard destroys it and sends the occupant flying.
In Wreck-It Ralph, the titular character finds a large ! while browsing a lost-and-found box in the Tapper tavern, which upon being picked up makes the characteristic "alert" sound from the Metal Gear series, and is thrown aside.
In League of Legends, Champions get an exclamation point over their head when the Champions Evelynn or Rengar, with his ability Thrill of the Hunt active, are nearby and stealthed.
In PlayStation All-Stars Battle Royale, the exclamation point appears when Metal Gear RAY sees a fighter. Once that happens, it will start an attack. The exclamation point appears again when Raiden is fighting Polygon Man in the final battle.
During a sneaking mission in Saints Row 4 , if players shoot out the marked lights, the alert sound plays and WTF! appears and flashes over the enemy's head.
In the Chinese version of Plants vs. Zombies 2: It's About Time, if a regular Kung-Fu or a Monk Zombie is attempting to grab a weapon from the Weapon Stand, an exclamation point will appear first, grab the weapon, then transform into a different zombie.
In the My Little Pony: Friendship is Magic episode "Make New Friends But Keep Discord", Discord attempts to conceal himself from Pinkie Pie inside a familiar looking cardboard box. Pinkie enters the frame and immediately exclaims, "Oh hi, Discord!", causing an exclamation point to briefly appear over his hiding place.
In the Monster Hunter series, creatures will have an exclamation mark over their head if they spot the player.
In the announcement trailer for Solid Snake, Raiden, and Naked Snake's appearances in Super Bomberman R, the Exclamation point, alongside the alert sound effect, are seen and heard, respectively when the cardboard box is removed to reveal a bomb underneath.