Colonel John Casey (Adam Baldwin) carries a custom SIG-Sauer P229 as his sidearm. The SIG is fitted with Crimson Trace laser grips, and with the flat surfaces polished on the slide, as well as the controls, trigger, and hammer. According to dialogue from "Chuck Versus the Colonel", the gun is a 9mm. Many have confused this gun with the SIG-Sauer P229R Equinox pistol (especially elsewhere on the net). The two pistols are displayed here for comparison. Morgan Grimes (Joshua Gomez) is trained with this exact same weapon in "Chuck Versus the Role Models" (S3E15), which he identifies as a "SIG 229, 9mm, full metal jacket, with laser grips". He then explains that he learned about guns from playing first-person shooter video games.
SIG-Sauer P229R
When Chuck (Zachary Levi) takes his "Red Test" in Season 3's "Chuck Versus the Final Exam" (S3E11), he is given a brand-new SIG-Sauer P229R. It appears that this will be his issued sidearm now that he is a spy. He is seen with it in Season 3's "Chuck Versus the Other Guy" (S3E13).
SIG-Sauer P239
CIA Agent Alex Forrest (Tricia Helfer) is seen cleaning and wielding a two tone SIG-Sauer P239 in Season 2's "Chuck Versus the Broken Heart" (S2E18).
In Season 1's "Chuck Versus the Wookie" (S1E04), Carina (Mini Anden) opens the trunk of her car to reveal several weapons, one being a Smith & Wesson 3913 "Ladysmith". This gun was later used by Jill Roberts (Jordana Brewster) in Season 2's "Chuck Versus the Gravitron" (S1E08).
IMI Jericho 941
La Ciudad's bodyguard holds his Jericho 941 to Chuck's back in "Chuck Versus the Tango" (S1E03). In the same episode, a stainless Jericho is pointed at Chuck by Uri (Matthew Willig), another of La Ciudad's bodyguards before Casey knocks him out with a microwave. Sarah dual-wields a blued and a stainless Jericho at "Weap-con" in Season 3's "Chuck Versus the Nacho Sampler" (S3E06).
IMI Desert Eagle Mark I
Peyman Alahi and his henchmen draw their Chrome Silver and Golden IMI Desert Eagle Mark I throughout "Chuck Versus the Wookie" (S1E04). It is very likely that the gold Desert Eagle wielded by Peyman Alahi was one of the same guns built for Austin Powers in Goldmember, although the ivory grips were removed for this show. Independent Studio Services, the armorers who supplied the weapons for Chuck, also supplied weapons to Goldmember. Casey uses a similar gun, possibly the same one, at Weap-con in "Chuck Vs. the Nacho Sampler." Sarah takes a stainless steel Desert Eagle with her on a mission in "Chuck Vs. the Anniversary" but is not seen using it. The same Desert Eagle is used in "Chuck Vs. Phase Three" Morgan Grimes (Joshua Gomez) is seen with one fitted with a scope and a custom compensator that matches the barrel. Although John Casey (Adam Baldwin) said it didn't have any bullets; it may have implied he only gave him blanks or none at all.
Beretta 950 Jetfire
A Beretta 950 Jetfire with nickel plating and pearl grips is used by the Flight Attendant Assassin (Josie Davis) in Season 3's "Chuck Versus First Class" (S3E05). She notably shoves the barrel up Chuck's nose. This is most likely the same gun that was used by Eva Mendes in The Spirit, since ISS supplied the weapons for that movie, as well as this series.
Beretta 90-Two
The Beretta 90-Two is the weapon of choice for Mary Bartowski (Linda Hamilton), Chuck's mother. It is first seen in the promo for "Chuck vs. the Aisle of Terror." She wields it in a standoff with Sarah and to shoot Chuck in a restaurant. She uses it equipped with an extended magazine.
Colt Mark IV Series 80 (Stainless)
In "Chuck Versus the Wookie" (S1E04), Carina (Mini Anden) opens her car's trunk to reveal several weapons, one being a stainless Colt Mark IV Series 80. In "Chuck Versus the Pink Slip" (S3E01), Chuck (Zachary Levi) holds the stainless Colt in the opening mission.
FN Five-seveN
The FN Five-seveN is the weapon of choice for operatives of the Ring. Equipped with tactical lights on their rails, Ring spies use the FN Five-seveN in "Chuck Versus the Ring" (S2E22). A similar weapon with a laser sight is also used by Ring operative Javier Cruz (Adoni Maropis) in "Chuck Versus the Pink Slip" (S3E01) and by Sydney Prince (Angie Harmon) in "Chuck Versus Operation Awesome" (S3E04).
Glock 17
Laszlo Mahnovski disarms Agent Scary of his Glock 17 in the opening scene of "Chuck Versus the Sandworm" (S1E06). Several Glock 17's are also used by Fulcrum agents in "Chuck Versus the Colonel."
An undercover MI-6 agent is carrying a suppressed Heckler & Koch USP in "Chuck Versus the Tango" (S1E03). Also, one of the sheik's associates wields this pistol in "Chuck Versus the DeLorean" (S2E10). In Season 3's "Chuck Versus the Honeymooners" (S3E14), Sarah and Chuck are threatened by operatives that carry the USP's with stainless slides. Sarah is later seen holding the weapon.
Heckler & Koch USP Compact
In Season 3's "Chuck Versus the Living Dead" (S3E17), Ellie (Sarah Lancaster) retrieves a two tone Heckler & Koch USP Compact from a speaker box she received from Ring agent Justin Sullivan (Scott Holroyd) when she hears someone in the house.
In "Chuck Versus the Angel de la Muerte" (S3E03), several soldiers that accompany Premier Alejandro Goya (Armand Assante) wield nickel plated Makarov PM pistols. Goya's chief bodyguard pulls his Makarov to force Chuck to perform a medical operation.
Norinco Type 54 / Model 213
Two nickel-plated Norinco Type 54s are used by Mei-Ling Cho (Gwendoline Yeo) while trying to free her brother from the Chinese mafia in "Chuck Versus the Sizzling Shrimp" (S1E05). Later in the episode, she uses this pistol to hold Chuck at gunpoint. (Bizarrely, while observing from inside their SUV, Casey somehow mistakes these twin pistols for Glocks. After a flash, Chuck corrects Casey, explaining that they are "Chinese Army-issue pistols".)
Ruger KP90
In Season 1's "Chuck Versus the Tango" (S1E03), La Ciudad (Lorena Bernal) uses a suppressed Ruger KP90 during the shootout at the art auction.
Bryce Larkin (Matthew Bomer) holds a Taurus PT92AFS at Chuck and Sarah after breaking into Casey's apartment in "Chuck Versus the Nemesis" (S1E10). Sarah also wields one in "Chuck Versus the Alma Mater".
Walther P5
In "Chuck Versus the Undercover Lover" (S1E12), Ilsa Trinchina (Ivana Milicevic) pulls a silver Walther P5 on Casey.
Submachine Guns
Heckler & Koch MP5A2
In the pilot episode as Bryce Larkin is stealing the Intersect computer, all members of CIA S.W.A.T. are carrying the Heckler & Koch MP5A2 with SureFire dedicated forend weaponlights. In "Chuck Versus Phase Three" (S4E09), Casey (Adam Baldwin) can be seen with a MP5A2 with an ACOG scope as well. Later in the same episode, Sarah also uses the MP5A2.
Heckler & Koch MP5K
CIA undercover agents carrying Heckler & Koch MP5Ks come to back up Casey and Sarah in "Chuck Versus the Alma Mater" (S1E07).
Micro Uzi
La Ciudad's two henchmen fire Micro Uzis at Casey and Sarah as they come to rescue Chuck in the hotel room in "Chuck Versus the Tango" (S1E03).
MAC-10
Many of the assassins in the restaurant in "Chuck Versus the First Date" are armed with MAC-10 submachine guns.
Rifles
Colt M4A1 Carbine
An armed sentry (presumably US Army) is seen holding a Colt M4A1 in "Chuck Versus the Helicopter" (S1E02). Members of the CIA strike team can also be seen carrying the M4A1, often outfitted with a variety of optics (Trijicon 4x ACOG scope, Aimpoint CompM2 red dot, and/or EOTech 552 holographic weapon sight), and SureFire tactical weapon lights. The same gun can be seen in the episode "Chuck Vs. Phase Three" John Casey (Adam Baldwin) switches out an MP5A2 for the M4A1 Carbine with an Trijicon 4x ACOG scope and with a vertical foregrip. It is only seen for a brief moments while getting into the truck to go find chuck (Zach Levi) and storming into the building.
AKMSU
In Season 3's "Chuck Versus the Angel de la Muerte", Premier Alejandro Goya's soldiers carry AKMSUs with full black furniture. Sarah also is seen holding one in the episode.
Heckler & Koch G36C
Criminals use the Heckler & Koch G36C, equipped with various accessories (one has a suppressor) in "Chuck Versus the First Date" (S2E01).
Valmet M76F
One of Stavros Demitrios' henchmen is seen firing a Valmet M76F with folding tubular stock in "Chuck Versus the Imported Hard Salami" (S1E09).
AKM
"The best Commie rifle ever made, Comrade AK-47" is used by Casey in "Chuck vs. the Anniversary" while escaping from Volkoff's headquarters. More AK-47/AKM's can be seen in the episode "Chuck vs. Phase Three".
SIG SG-552
In "Chuck Versus the Seduction Impossible", Fatima Tazi's henchwomen are armed with SIG 552.
Sniper Rifles
Sako M995 TRG-S
Malena (Lorena Bernal), aka "La Ciudad", is seen on the roof of the Wienerlicious with a scoped and suppressed Sako M995 TRG-S sniper rifle in "Chuck Versus the Tango" (S1E03).
Blaser R93 Sniper Rifle
In Season 3's "Chuck Versus the Three Words" (S3E02), hitman Karl Stromberg (Vinnie Jones) uses a Blaser R93 Sniper Rifle to wound a man who stole his case. (The name is a reference to the main villain in the James Bond film The Spy Who Loved Me).
AIG Asymmetric Warrior ASW338LM
In Season 3 Episode 8 The Fake Name where Chuck must take the identity of the world's most dangerous assassin for a job that some old school spy's hired Rafe Gruber that Chuck must be. Later on in the episode Chuck is supposed to use the ASW338LM to shoot Shaw, also Sarah is in the room then he leaves and later the real Rafe Gruber tries to use it but then goes and tries to kill Chuck, Shaw, and Sarah. Then John Casey saves them with the snipers and says apparently he's one of 5 people in the world that can make that shot.
Shotguns
Ithaca 37
In Season 3's "Chuck Versus the Angel de la Muerte", Casey is seen taking out a Ithaca 37 with a nickel finish, pistol grip and extended mag barrel from a hidden compartment in his apartment. The shotguns are on the left in the compartment. Chuck tosses the Ithaca 37 to Sarah in the episode.
Mossberg 500 Mariner
In addition to the Ithaca, Casey grabs a Mossberg 500 Mariner fitted with a pistol grip and saddle shell holder.
Short-barreled shotgun
Ted Roark (Chevy Chase) takes a concealable shotgun from a fellow Fulcrum agent while attacking Ellie and Devon's wedding in "Chuck vs. the Ring."
Machine Guns
Handheld M134 Minigun
Preparing to leave Castle, John Casey packs up a Minigun, lamenting that he never got to use it. He later uses it while rescuing Sarah and Chuck from a Ring facility in "Chuck vs. the Pink Slip."
Trivia
Throughout several episodes of the show, usually whenever Chuck "flashes" on gun-runners or other criminals, the Intersect shows him pictures of large armory rooms full of guns. All of these images are pictures of the weapons vault of Independent Studio Services, the company which supplies the weapons and other props used on Chuck. If you've ever been curious to know what a Hollywood prop house's armory looks like, now you know!