Theo (Michael Ealy) enters in a hospital with a Glock 19 while looking for medical supplies in "Reunion" (S3E06).
Glock 17
FBI Agent Mike Weston (Shawn Ashmore) continues to carries a Glock 17 as his chief sidearm, which he has used since Season 1. FBI Agent Max Hardy (Jessica Stroup) also carries the Glock. Mike and Max are armed with they Glocks to enter in the Andrew's house during "New Blood" (S3E01). In the same episode, several corpses are seen with Glocks, representing the death of some characters in the second season.
Daisy (Ruth Kearney) carries a suppressed SIG-Sauer P232 given by Julianna when she tries to get into a room in "A Hostile Witness" (S3E05).
SIG-Sauer P239
In "New Blood" (S3E01), Max Hardy (Jessica Stroup) is briefly seen firing her SIG-Sauer P239 during a flashback from the Season 2. Ryan carries a SIG P239 during "The Hunt" (S3E07). Most notably when Ryan fires it at the end of episode.
Assault Rifles
Colt M4A1
The FBI SWAT agents are seen using Colt M4A1s fitted with railed handguards, vertical grips and Aimpoint red dot sights throughout the series.
AKMSU
Spider (John Keating) is seen firing what appears to be an AKMSU with RIS handguard in "Boxed In" (S3E02).
Sniper Rifles
Remington 700 PSS
In "A Hostile Witness" (S3E05), Mark (Sam Underwood) is seen with a Remington 700 PSS. He fires it when tries to defend himself from Mike.
Shotguns
Remington Model 870
In "Reunion" (S3E06), Theo (Michael Ealy) borrows a Remington 870 from his internet friend and uses it later in a bank.