Colonel John Casey (Adam Baldwin) carries a custom SIG-Sauer P229 as his sidearm, equipped with Crimson Trace laser grips, and with the flat surfaces polished on the slide, as well as the controls, trigger, and hammer. 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.
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).
IMI Jericho 941
La Ciudad's bodyguard holds his Jericho 941 to Chuck's back in "Chuck Versus the Tango" (S1E03).
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 Peman 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.
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."
Glock 17
Laszlo Mahnovski disarms Agent Scary of his Glock 17 in the opening scene of "Chuck Versus the Sandworm" (S1E06).
Taurus PT92
Bryce Larkin holds his Taurus PT92 at Chuck and Sarah after breaking into Casey's apartment in "Chuck Versus the Nemesis" (S1E10).
Weapon originally misidentifed as a Beretta 92FS Inox. Berettas have the safety on the top of the slide; it's visible even from a distance. -MT2008
FN Five-seveN
Equipped with tactical lights on their rails, Fulcrum spies use the FN Five-seveN in "Chuck Versus the Ring" (S2E22).
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 weapon lights.
Heckler & Koch MP5K
CIA sleeper 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).
Assault Rifles
Colt M4A1 Carbine
An armed sentry, presumably US Army, is seen holding a Colt M4A1 in "Chuck Versus the Helicopter" (S1E02). CIA S.W.A.T. 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.
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 M76
One of Stavros Demitrios' henchmen is seen firing a Valmet M76 in "Chuck Versus the Imported Hard Salami" (S1E09).