What appears to be a Beretta 92FS Inox was handed to Kramer Daly in "Sister's Keeper" (S1E06). This pistol has a black safety switch and mag release lever, making it likely that this is a Kimar replica.
Smith & Wesson SW1911SC E-Series
Archer Petit (Billy Brown) carries what appears to be a Smith & Wesson SW1911SC E-Series as his main sidearm, first used in the beginning of "Truth and Consequences" (S1E05).
Glock 17
Metropolitan Police Department officers are armed with Glock 17s as their main sidearm, first seen near the end of "Truth and Consequences". One is used by a gunman in the middle of "Fight or Flight". An assassin uses one with a suppressor to search for Morgan Sanders with gunmen working for Colonel Thomas Blair are armed with unsuppressed Glock 17s in "Suspicious Minds".
Glock 19
A Glock 19 was used by a bank robber in "Pilot". A Secret Service agent appears to use a Glock 19 as his main sidearm near the end of "Endgame".
Heckler & Koch USP
One of Colonel Blair's men has a Heckler & Koch USP in his duty holster in "Suspicious Minds".
Heckler & Koch USP Compact
A Heckler & Koch USP Compact was used by Kramer as his main sidearm, first seen in a robbery in "Sister's Keeper". Another one is used by Special Agent Carlisle as he forces Dr. Ellen Sanders to handle a suppressed USP Compact in the same episode.
Heckler & Koch USP Tactical
A Heckler & Koch USP Tactical is used by Sandrine Renault aka Maria Gonzales (Sandrine Holt) as her main sidearm in the season.
SIG-Sauer P226
A SIG-Sauer P226 or P226R is used by Sandrine when she goes with Duncan and the others to New York in "Off the Record".
SIG-Sauer P229R
A SIG-Sauer P229R is used by FBI Special Agent Duncan Carlisle (Dylan McDermott) in the season. He later uses a two-tone version of it when he leads an invasion to seize the Sanders family as hostages in the season. Unfortunately, his sidearm is briefly stolen by armed kidnappers hired to abduct him near the end of "Off the Record".
SIG-Sauer P230
A blued SIG-Sauer P230 appears to be used by an armed woman to restrain Carlisle near the end of "Off the Record".
Smith & Wesson 4506
A Smith & Wesson 4506 was used by Herman in "Loose Ends".
Walther PPK
What appears to be a Walther PPK is used by an armed guard when he confronts Sandrine in "Sister's Keeper". Burton Delaney (Larry Pine) briefly uses one with a mounted suppressor in case Kate Renner would object to his proposal to not tell his daughter on the origin of her birth in "Off the Record".
Revolvers
Smith & Wesson Model 65
Dr. Sanders acquires a Smith & Wesson Model 65 revolver before her sister Lauren finds out about it in "Sister's Keeper" (S1E06). Agent Carlisle hands Brian Sanders a Smith & Wesson Model 65 to defend himself in "Suspicious Minds" (S1E14).
Submachine Guns
Heckler & Koch MP5A3
Kramer Daly (Rhys Coiro) and Archer Petit (Billy Brown) use Heckler & Koch MP5A3 submachine guns with Surefire tactical lights mounted underneath the barrels when they seize control of the Sanders residence in "Pilot". Secret Service agents and a few MPD Emergency Response Team assaulters use them when the hospital is "attacked" near the end of "Endgame".
Heckler & Koch MP5A4
At least one MPD ERT assaulter is armed with the Heckler & Koch MP5A4 when they seize control of the OR near the end of "Endgame".
A Double Barreled shotgun is used by Kate Renner (Maureen Mueller) when she confronts Dr. Sanders in the middle of "Burden of Truth". A sawed-off double barreled shotgun us used by Herman as his main weapon to attempt a drive-by shooting in "Loose Ends".
A Nemesis Arms Vanquish is used by a hired assassin in the beginning of "Power of Persuasion". A mercenary uses a suppressed Nemesis Arms Vanquish in the middle of "Off the Record".
Remington 700PSS
A Remington 700PSS is used by a MPD ERT sniper in "Pilot" (S1E01), most notably to take out one of the bank robbers.
Other
X26 Taser
Archer uses a X26 Taser pistol to take out a mercenary non-lethally in the middle of "Off the Record".
M84 Stun Grenade
A M84 stun grenade is used by Leroy and his men near the end of "Endgame" to create a distraction.
Arsenal
A cache of small arms were found by MPD officers near the end of "Truth and Consequences".