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.
SIG-Sauer P220 (Stainless)
A stainless SIG-Sauer P220 is seen in inside one of Carina's briefcases in "Chuck Versus the Wookie" (S1E08).
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". Jill Roberts (Jordana Brewster) pulls a Ladysmith on Chuck in "Chuck Versus the Gravitron" (S2E08).
Smith & Wesson 6906
In "Chuck Versus the Marlin" (S1E13), Sarah has Chuck pull her backup Smith & Wesson 6906 from the horseradish jar at the Wienerlicious.
Colt Gold Cup National Match (Stainless)
In "Chuck Versus the Wookie" (S1E04), Carina (Mini Anden) opens her car's trunk to reveal several weapons, one being a stainless Colt Gold Cup National Match.
Kimber Custom TLE II
A Kimber Custom TLE II is seen in Carina's (Mini Anden's) trunk in "Chuck Versus the Wookie" (S1E04).
Colt M1911A1 (Nickel)
The assassin Lizzie (The Pita Girl), pulls a suppressed bright nickel Custom M1911A1 on Sarah in "Chuck Versus the Marlin" (S1E13).
Glock 17
Laszlo Mahnovski disarms Agent Scary of his Glock 17 in the opening scene of "Chuck Versus the Sandworm" (S1E06).
Heckler & Koch VP70
A Heckler & Koch VP70 is seen in the hands of Chinese mafia in "Chuck Versus the Sizzling Shrimp" (S1E05).
IMI Jericho 941
La Ciudad's bodyguard holds his Jericho 941 to Chuck's back in "Chuck Versus the Tango" (S1E03).
IMI Jericho 941 (Stainless)
Uri (Matthew Willig) holds the stainless Jericho on Chuck in "Chuck Versus the Tango" (S1E03) before Casey knocks him out with a microwave.
IMI Desert Eagle Mark I
Peyman Alahi and his henchmen draw their Chrome Silver and Gold 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 series. Independent Studio Services, the armorers who supplied the weapons for Chuck, also supplied weapons to Goldmember.
Makarov PM
Several guests at Viktor Federov's Wedding pull their Makarov's when facing Sarah in Season 1's "Chuck Versus the Undercover Lover".
Norinco Type 54 / Model 213
Two nickel-plated Norinco Type 54s are used by Mei-Ling Chou (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".)
Tokarev TT-33
Sarah crashes Viktor Federov's wedding and takes a Tokarev TT-33 Pistol off a guest in Season 1's "Chuck Versus the Undercover Lover".
Ruger KP90
In "Chuck Versus the Tango" (S1E03), La Ciudad (Lorena Bernal) uses a suppressed Ruger KP90 during the shootout at the art auction.
Taurus PT92AFS
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.
Walther P99
What appears to be a heavily customized Walther P99 is featured prominently in "Chuck Versus the Imported Hard Salami" (S1E09). The weapon is also seen hanging in Casey's apartment arsenal as well as in the Castle. Since the handgun isn't seen fired, the P99 is most likely the Walther Nighthawk, a CO2 airgun.
Submachine Guns
Heckler & Koch MP5A2
In the pilot episode as Bryce Larkin is stealing the Intersect computer, numerous members of the CIA's security detail carry the Heckler & Koch MP5A2 with SureFire dedicated forend weaponlights.
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).
Uzi
A guard is seen armed with an Uzi while overseeing the transport of a shipping container in Season 1's "Chuck Versus the Imported Hard Salami".
Rifles
Colt M4A1 Carbine
An armed sentry (presumably US Army) is seen holding a Colt M4A1 in "Chuck Versus the Helicopter" (S1E02). In several episodes, 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.
Valmet M76F
One of Stavros Dmitrio's henchmen is seen firing a Valmet M76F with folding tubular stock in "Chuck Versus the Imported Hard Salami" (S1E09).
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).
Other
M2 84mm Rocket Launcher (Carl Gustav Recoilless)
Lon Kirk fires a mockup of an M3 Carl Gustav Recoilless Rifle identified in the episode as an "M2 84mm Rocket Launcher" by Casey, at a ship carrying not only counterfeiting plates, but also Morgan and Anna in "Chuck Versus the Crown Vic" (S1E11). This prop appears to be the same one used in the series NCIS and NCIS: Los Angeles.
Tranquilizer Weapon
In Season 1's "Chuck Versus the Helicopter", another tranquilizer dart weapon appears, and looks to have been built up from an M16-type receiver. This same Tranquilizer gun was earlier used to tranq Casey.
Palmer Cap-Chur Short Range Projector
Another is seen at the Weap-Con in "Chuck Versus the Nacho Sampler".
Armories and Gun Displays
"Castle"
"Castle", is the code name for the underground CIA/NSA substation where Sarah, Casey, Chuck, and Morgan communicate with their superiors (mainly General Diane Beckman). Castle is located underground somewhere between the former Orange-Orange and the current Buy More. It is comprised of a main area for team debriefing, a video conference room for federal debriefs comprised of a series of large computer screens, 2 prisoner wings (1 solitary, 1 bulletproof acrylic holding cells), 1 interrogation wing, a Dojo for martial arts practice, an armory with a huge selection of weapons including 3+ Casey custom SIG P229s, a shooting range, and a scientific analytical labratory, 1 wing that was used for the National Clandestine Service with maximum security holding cells, now it is used as a maximum security prisoner holding facility, and recently revealed in "Chuck Versus Agent X", a room for secret vehicle development.
Gunrunner Armory
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!