The Glock 17 returns as the standard sidearm of all police officers in the Portland Police Bureau. FBI agents use them also as their main sidearm, which is prominently seen in "Bad Teeth". Juliette (Bitsie Tulloch) takes Renard's sidearm in "Face Off".
Heckler & Koch USP
A gunman working for Mia Gaudot is armed with a Heckler & Koch USP in "Over my Dead Body".
=M1911A1
A hired assassin (Danny Hart Donoghue) opens fire with a M1911A1 at Cole Pritchard and Krystal Fletcher near the end of "Natural Born Wesen". This model is likely a flashpaper variant since the pistol was fired at the actor at very close range, which would make blank .45 ACP bullets very dangerous to use when up close.
Walther PPK
An assassin chambers a bullet in what appears to be a Walther PPK in "Nameless".
What appears to be a Smith & Wesson 66 is used by a Skalengeck gunman after shooting Angelina in "Over my Dead Body".
Submachine Guns
Heckler & Koch MP5A3
Portland Police Bureau Special Emergency Response Team (SERT) operators use Heckler & Koch MP5A3s in "The Hour of Death".
Heckler & Koch MP5A4
SERT operators raid Mt. Talapus armed with Heckler & Koch MP5A4s in "The Bottle Imp".
Heckler & Koch UMP
SERT operators use Heckler & Koch UMPs in "The Bottle Imp".
IMI Uzi
Gus Campbell (Eric Martin Reid) uses an IMI Uzi in a bank robbery in "Natural Born Wesen".
Shotguns
Elephant Gun
Monroe (Silas Weir Mitchell) is armed with a double barrel-based Elephant Gun as seen in the introduction. Hank handles the same gun in "The Bottle Imp".
Remington 870 Folding Stock
Hank uses a Remington 870 Folding Stock shotgun in season 2, starting from the episode "Bad Teeth".
Battle Rifles
Springfield M1A
Bill Granger (Josh Stewart) uses a M1A with a scope and a sling in "The Bottle Imp".
Bolt-Action Rifles
Remington Model 700
One of the Walkers uses a Remington Model 700 in "Bad Moon Rising", but was never fired.
Others
Doppelarmbrust
The Dopppelarmbrust returns in "Bad Teeth" as the weapon used by Nick to take down Akira in his house, since it connects with the final episode of the 1st season. It's also prominently seen in the introduction, taken from "Leave it to the Beavers" while being mixed in with other screenshots. It's seen again in "The Bottle Imp" and in "The Hour of Death".
X26 Taser
A X26 Taser is seen in the holster of a Portland Police Bureau officer in "Quill".