S.T.A.L.K.E.R.: Clear Sky is a 2008 video game and the prequel to S.T.A.L.K.E.R.: Shadow of Chernobyl. While the gameplay and engine are essentially the same with some more polish and content cut from the original, it also features some brand new plot, some new characters, and "new" firearms (all of the "new" guns are actually guns cut from SoC).
Clear Sky also introduces a new system: weapon upgrades; upgrades are installed by technicians, who can also repair your weaponry. Upgrades do not change the appearance of the weapon, and as such will not be noted.
Note: As the weapon models are largely identical to Shadow of Chernobyl, please see that page for a more detailed overview on how weapons are depicted throughout the series in general.
The following weapons appear in the video game S.T.A.L.K.E.R.: Clear Sky:
The Beretta 92FS appears in-game as the "Martha". Unlike SoC (in which there was only one in the entire game), the weapon is now far more widespread. Its stats have also changed, now being more suited for slow rapid-fire.
Browning Hi-Power Mark III
Originally cut from SoC, the Browning Hi-Power Mark III appears in-game as the "HPSS-1m". It is fairly common, and is an all-around average pistol, not excelling in any particular niche. A variant known as the "HPCS-1" was cut from the game, and would've featured higher reliability.
Colt M1911
The Colt M1911 appears in-game as the "Kora-919". It has received a considerable upgrade from its SoC incarnation, now being one of the most accurate pistols in the game.
Desert Eagle Mark XIX
The Desert Eagle Mark XIX appears in-game as the "Black Kite". It is used primarily by the Bandits, and can only be bought from them. It is still incorrectly chambered in .45 ACP. A unique variant known as the "Modified shooter" has multiple upgrades pre-installed and is the target of a quest. The "Big Ben" from the previous game was planned to make a return, but got cut from the game; it would've no longer used 9x39mm, but was to feature an unspecified barrel attachment.
Fort-12
The Fort-12 returns under the different name of "Fora-12". It is fairly similar to its SoC counterpart, being a decent upgrade to the Makarov PM but being less reliable, noticeably jamming more often. A variant known as the "Fora-14" was cut from the game, and would've been similar to the "Fort-15" from SoC, sporting a larger magazine.
Heckler & Koch USP Compact
The Heckler & Koch USP Compact appears in-game as the "UDP Compact". It has the highest rate of fire out of all of the handguns. A variant of the USP called the ".223 Pistol" (referencing the Fallout weapon of the same name) was cut from the game; as its name suggests, it chambers the unused .223 round and would've been very powerful, but has a lowered 5 round capacity.
Makarov PB
The Makarov PB appears in-game as the "PB1s". Unlike its SoC incarnation, it is very rare, only able to be bought or found in stashes. To make up for it however, it is now the most accurate pistol in the game.
Makarov PM
The Makarov PM appears in-game as the "PMm". It is given to Scar by Docent Suslov as the starting secondary weapon, and has also been given a noticeable upgrade since SoC, as its damage has been given a slight boost; its accuracy, however, is still not very good. A unique one known as the "Inscribed pistol" is the target of a quest; this variant is identical to the standard PM, aside from its name and description.
SIG-Sauer P220
The SIG-Sauer P220 appears in-game as the "SIP-t M200". It is somewhat rare, only being used by Mercenaries. Performance-wise, it is fairly similar to the USP Compact, but has a lower rate of fire and a slightly too large 10-round capacity.
Walther P99
The Walther P99 appears in-game as the "Walker P9m". It is much rarer than in SoC, as most stalkers now seem to use the Beretta 92FS or the Hi-Power as their 9x19 pistol of choice, only becoming readily available in Limansk from dead Monolith troops.
Submachine Guns
Heckler & Koch MP5A3
The Heckler & Koch MP5A3 appears in-game as the "Viper 5", and returns as the sole submachine gun. The player will most likely first encounter it in the hands of a Renegade in the swamps, and will frequently find it again later on as a low-level primary weapon. A version with higher muzzle velocity known as the "Viper 5m" was cut from the game.
Assault Rifles
AKMSU
The AKMSU appears in-game as the "Akm-74/2U". It is considerably less accurate than in Shadow of Chernobyl, and is the weakest assault rifle available. It is still depected as using 5.45x39mm ammunition rather than the correct 7.62x39mm.
AKS-74
The AKS-74 appears in-game as the "Akm-74/2". Oddly, one will be in Scar's inventory by default, even though 5.45 ammunition is unlikely to be encountered until the player reaches the Cordon. It can mount a GP-25 grenade launcher, but only after an upgrade; it is somewhat strange that it and the AN-94 require upgrades to mount one, as they should be able to by default. A unique version called the "Trophy AKM-47/2" can be found hidden in a building in the Cordon, and rather implausibly fires 7.62x54mmR; while conversions of AK variants to 7.62x54mm are possible, the in-game model is completely unmodified, and most notably still uses a standard 5.45 AK-74 magazine, which wouldn't even fit a 7.62x54mm round inside of it. Another version of the weapon named the "Akv 74" was cut from the game, and had a higher rate of fire but was unable to accept scopes.
AN-94
The AN-94 appears in-game as the "AC96/2". It is used mostly by Duty, the military, and the Monolith; the second of those in the list will likely be the player's first encounter with the weapon, as it used by the soldiers near the entrance to the Cordon from the swamps. Like the AKS-74, it can only mount a GP-25 after an upgrade. A unique variant called the "Duty member's assault rifle" is the target of a quest. Another unique variant with an integrated suppressor was to be included in the game, named the "AC96sl".
AS Val
The AS Val returns under the different name of "SA Avalanche". The earliest one may be able to acquire it is through buying it from the Bandits' trader, Tooth, but later on it will become more common.
Enfield L85A1
The Enfield L85A1 appears in-game as the "IL 86". It appears as a common weapon amongst Freedomers and veteran stalkers. It can rather oddly mount the SIG GL 5040 after an upgrade. A version with more muzzle velocity called the "IL86s" was cut from the game.
FN F2000
An FN F2000 with an attached FN GL-1 reappears in the game as the "FT 200M", and as the highest-tier asssault rifle. A variant referred to as the "FT 202M", which would've traded the grenade launcher for a "gravitational bullet stabilizer" allowing for more accurate fire, was cut from the game.
Heckler & Koch SL8-1
A Heckler & Koch SL8-1 modified to resemble a G36 returns from the previous game as the "GP 37". It is one of the highest-tier weapons in the game, but is beaten out by the F2000 above. It is significantly rarer than in the previous game, only able to be acquired by completing the Bandits' faction war or by completing a randomly-given quest to find a specific artifact. It can mount the SIG GL 5040 after an upgrade.
OTs-14-4A Groza
The OTs-14-4A Groza appears in-game as the "Tunder S14". It is rarer than in Shadow of Chernobyl, with Duty being the only user of the weapon for most of the early game; appropriately, one will be given for free if the player decides to join Duty. A version known as the "Tunder S14sn" was cut from the game; it is vaguely described as a "sniper prototype" of the regular weapon.
SIG SG 550
The SIG SG 550 appears in-game as the "SGI 5k". It is essentially Freedom's equivalent to the OTs-14 Groza, being used almost exclusively by them and will be given for free to the player if one decides to join Freedom. It can mount the SIG GL 5040, but only after an upgrade; it is rather strange that it needs an upgrade in order to mount one, as the GL 5040 was designed specifically for this rifle. A version firing 5.45x39mm ammunition called the "SGI 5.45" was cut from the game.
Z-M LR 300ML
The Z-M LR 300 appears in-game as the "TRs 301". It remains the most common 5.56 rifle, and is frequently used by a variety of factions. It can also mount a SIG GL 5040 after the appropriate upgrade is installed. A version similar to the "Sniper TRs 301" from SoC would've been included as the "TPs 'Left-hander'", featuring higher accuracy in exchange for a lower rate of fire.
Sniper Rifles
SVD Dragunov
The SVD Dragunov appears as the "SVDm 2". It can be acquired by buying it from Ashot (Freedom's trader), or scavenging it from fallen Freedom and Monolith snipers. Similarly to the USP Compact, a variant of this weapon referencing the Fallout weapon known as the "Bozar" was cut from the game; it fires the same .223 round, has a 300-round magazine, and fires 10 rounds at the same time in a strange shotgun-like manner. If the Bozar is viewed in the inventory, it appears as a PK, a result of it being built off the machine gun's codebase.
SVU Dragunov
The SVU Dragunov appears in-game as the "SVUmk2"; it is used exclusively by Freedom. The player can now sprint with it equipped. A version with lower recoil was cut from the game, known as the "SV-Am".
VSS Vintorez
The VSS Vintorez appears in-game as the "Vintar BC". It is prominently featured in the game's opening, and that same VSS can be found in the swamps near the entrance to Agroprom. The VSS is also used by a few stalkers in Agroprom. A variant cut from the game known as the "'Avalanche' Vintar" was to feature a doubled magazine capacity in exchange for a lower magnification scope.
Machine Guns
PK
The PK appears in the game as the "RP-74", a name oddly similar to the RPK-74. It is used primarily by Duty, but the bandits and the military also use it on rare occasions. The player can only hipfire the weapon, with the iron sights being completely inaccessible; it can also only use one type of 7.62x54mmR ammo. Mounted variants are sometimes also encountered; the one encountered when entering the Cordon for the first time is especially infamous, as Scar will be very underequipped for this occasion. A unique variant known as the "Tank machine gun" can be found in a T-64 in the Red Forest; this variant somehow holds a whopping 2000 rounds in its standard 100-round belt box. The description of the "Tank machine gun" and where it's found also implies that it is meant to be a PKT, but its model is still of a PK.
Shotguns
Mossberg Maverick 88
The Maverick Model 88 appears in-game as the "Chaser 13". It is somewhat more common than in the previous game, but is otherwise fairly similar to its previous incarnation. A unique (but functionally identical) variant called "A bandit's Chaser 13" is the target of a quest. Another variant, called the "'Freedom' Chaser", was cut from the game; this variant featured a rifled barrel, allowing greater accuracy when using slugs but disallowed usage of buckshot and darts.
Franchi SPAS-12
The Franchi SPAS-12 appears in-game as the "SPSA14". Unlike Shadow of Chernobyl, it is now operated in pump-action mode, with an appropriately slower rate of fire. A funtionally-identical unique version called the "Ripper shotgun" is the target of a quest given by a Duty member; according to its description, this variant comes from a limited-edition batch noted for its better finish. A variant known as the "SPSA-AUT" was cut from the game, which would've featured a higher 10-round capacity and a higher rate of fire.
TOZ-34
The TOZ-34 was originally cut from SoC, but has now been reintroduced as the "Hunting rifle"; its strange designation as a rifle is due to a mistranslation. It is a very common weapon, being used by rookies of various factions.
TOZ-66
A sawn-off TOZ-66 appears in the game as the "Shotgun". It is given by Suslov as a primary weapon, and can still be found very frequently later.
The RG-6 appears in the game as the "Bulldog 6". Like the previous game, it is incredibly rare, with only four existing in the game.
RPG-7
The RPG-7 appears in the game as the "RPG-7u". Like the RG-6 above, it is very rare, with its ammunition being even rarer; as before, its ammunition is misnamed, as it is a PG-7L rocket labelled as an OG-7V.
The F-1 hand grenade appears in the game as the "F1 grenade". It is rarer than the RGD-5 below, but deals more damage, and has a larger blast radius.
RGD-5
The RGD-5 hand grenade appears in the game as the "RGD-5 grenade". It is the most common grenade, and has a smaller blast radius and damage output than the F-1.
The "EM1 Rifle" (likely referencing the EM-1 from the film Eraser) is a prototype version of the "Gauss Rifle" that would be seen in the other games. Unlike the Gauss Rifle, it does not fire bullets, but rather extremely strong electromagnetic bursts powered by fragments of the Flash artifact; as such, it does very little damage to live targets, but deals much more to electrical devices.