The Glock 17 pistols, including the simunition models, are seen prominently in the hands of FBI agents and the recruits in the show as a likely stand-in for the Glock 22, the standard sidearm of the FBI agents in reality.
Glock 19
The Glock 19 is used by FBI Special Agent Jordan Kent (Patrick Labbé) as his main sidearm in the season.
Colt Gold Cup National Match Enhanced
Recruits are seen firing what appears to be stainless Colt Gold Cup National Match Enhanced pistols at the Quantico range, which is not issued to the FBI agents in reality.
Colt M1911A1
The Colt M1911A1 is used by the FBI Academy when Alex and the other FBI trainees conduct simulated HRT hostage rescue operations in "Fast" (S01E19), which is a likely stand-in as the Springfield Armory TRP, the standard sidearm of the HRT agents in reality.
Colt XSE
A Colt XSE is used by a CIA agent in rural New York near the end of "Care" (S01E17).
Heckler & Koch P2000
A Heckler & Koch P2000 is used by a CIA agent in rural New York near the end of "Care" (S01E17).
IMI Desert Eagle
An IMI Desert Eagle is seen on a social media page during a briefing session in Quantico in "God" (S01E06).
Ruger KP89
What appears to be a Ruger KP89 is seen in a terrorist hideout in "Go" (S01E07)
Ruger KP94DAO
A Ruger KP94DAO was briefly used by Derrick (Jaa Smith-Johnson) to threaten Miranda and Charlie at the end of "Turn" (S01E15).
Ruger SR9c
A Ruger SR9c is used by Charlie Price (J. Mallory McCree) under duress to shoot at Miranda at the end of "Turn" (S01E15).
SIG-Sauer P226
A SIG-Sauer P226 with a cerakote green body is used by NAT trainee Drew Perales (Lenny Plat) in "Turn" (S01E15), mentioning that it was his personal sidearm.
Smith & Wesson 5944
What appears to be a Smith & Wesson 5944 is found by Nimah in a FBI-issued duffel bag near the end of "Fast" (S01E19).
Revolvers
Colt 1851 Navy
A Colt 1851 Navy is seen on display at a bar in "Turn" (S01E15).
Single Action Army
A Single Action Army revolver is seen on display at a bar in "Turn" (S01E15).
Smith & Wesson Model 36
A Smith & Wesson Model 36 with a nickel finish is used by a teenage Alex (Shoba Narayanan) to shoot her abusive father in a flashback in "Run" (S01E01).
Ruger SP101
A long-barrel Ruger SP101 is used by Simon in "Answer" (S01E14) while thinking about killing himself.
Submachine Guns
CZ Scorpion Evo 3 A1
A CZ Scoprion Evo 3 A1 is seen with the corpse of a terrorist in "Turn" (S01E15).
IMI Micro Uzi
An IMI Micro Uzi is used by a terrorist while breaching Quantico in "Turn" (S01E15).
Assault Rifles
M4A1 Carbine
The M4A1 is another prominent weapon featured in the show. It is used by FBI HRT operators and US Marines as their primary firearm.
Umarex T4E TM4
What appear to be Umarex T4E TM4s are used by FBI recruits and staff in training exercises.
Colt LE Carbine
The Colt Law Enforcement Carbine is used by Shelby Wyatt (Johanna Braddy) and Caleb Haas (Graham Rogers), who are seen firing them on the range at Quantico in "Run" (S01E01) as a stand-in for the M4A1. It's also used by the FBI as a stand-in for the M4A1.
Zastava M70B1
Near the conclusion of "Go" (S01E07), a terrorist is seen armed with an Zastava M70B1.
Zastava M70AB2
Near the conclusion of "Go" (S01E07), another terrorist is seen armed with an Zastava M70AB2.
AKS-74U
An AKS-74U is used by Hamza Kouri (Michael Aronov) when he engages Alex at the end of "Go" (S01E07).
What appears to be a Heckler & Koch G36KV is used by a SWAT operator in a flashback sequence in "Answer" (S01E14).
Colt Model 933
A Colt Model 933 is seen on a photo of a HRT operator in Multicam camo during a lecture session at the FBI Academy in "Kill" (S01E04) and later on in "Guilty" (S01E09), being used as an alternative to the M4A1 in close quarters.
M16A2
An M16A2 (or more likely an AR-15A2/HBAR, the civilian equivalent) is seen on a gun rack within Shelby Wyatt's home.
Shelby Wyatt (Johanna Braddy) can be seen firing a Knight's Armament SR-25 on the range at Quantico in "Run" (S01E01). One appears to be used by a HRT sniper near the end of "Found" (S01E05).
Remington 700PSS
A Remington 700PSS simunition model is used by the FBI during training sessions. FBI HRT/SWAT snipers use them as their main sniper rifle.
Remington 700
A Remington Model 700 appears to be held by Shelby on a magazine cover of Lock & Load in the middle of "Run" (S01E01). Simon uses it while living near the American-Canadian border in "Answer" (S01E14).
Grenades
Smoke Grenade
A smoke grenade was used in "Alex" (S01E12) by Natalie in the mock anti-terrorist exercise.
Other
FBI Academy Armory
The FBI Academy's armory is briefly shown in "Found" (S01E05).
Hidden Arsenal
A hidden room has an arsenal of small arms in "Answer" (S01E14).
Rubber Remington 870
A rubber-based Remington 870 is used by Iris during a close quarters training session in "Turn" (S01E15).
Small Arms on Table
Several pistols/revolvers were seen on a table being cleaned by the Amin siblings near the end of "Fast" (S01E19).