Dale Maddox's (Alan Tudyk) sidearm in the Pilot is a Gen 2 Glock 17, which Erica Evans (Elizabeth Mitchell) later confiscates from his unmarked FBI Ford Crown Victoria in "A Bright New Day".
Glock 19
Erica Evans' duty weapon from episode 2, "There is No Normal Anymore", onwards was a Gen 2 Glock 19. A Glock 19 was also used by Georgie Sutton (David Richmond-Peck) in "A Bright New Day" and "It's Only the Beginning".
Glock 26
A Glock 26 is used by Erica Evans in episode 12, "Red Sky".
A Ruger KP89 is used by Ryan Nichols (Morris Chestnut) as his main sidearm, seen first in "It's Only the Beginning". After a period without using it, Ryan is seen with it in episode 9, "Heretic's Fork".
SIG-Sauer P226
A nickel SIG-Sauer P226 is used by Cyrus to threaten Ryan in "A Bright New Day". Ryan uses the pistol for a while when he disarmed Cyrus. In Season 2, Kyle Hobbes (Charles Mesure) started carrying the nickel P226 as his sidearm of choice (replacing the Walther P99 he carried in Season 1).
A standard blued P226 is given to Val by Ryan to defend herself against the V soldier, though it looked like a Walther P99 when he passed to her.
A Smith & Wesson 3913 "Ladysmith" is used by Erica in "Welcome to the War" after her Glock gets chopped in half. It is only used in this episode; afterwards, she resumes using a Glock.
Kyle Hobbes (Charles Mesure) uses a Walther P99 in the face-off before the escape in "Welcome to the War". It's also his main sidearm. In the Season 2 episode "Siege", Ryan Nichols (Morris Chestnut) uses another P99 when he raids Eli Cohn's (Oded Fehr's) compound.
Jericho 941 R
A nickel-plated Jericho 941 R with a suppressor, is used in the attempted "assassination" of Marcus.
"Pre-B" CZ 75
Kyle Hobbes (Charles Mesure) gives a "Pre-B" CZ 75 to Jack which is then used by Jack to shoot the human sniper who takes out Alex in "We Can't Win", which becomes his main sidearm. A nickel CZ 75 is also used by Peter Combs (Craig Fraser) in "It's Only the Beginning."
Colt Lawman Mk III
Alex Caruso is armed with a Colt Lawman Mk III in "We Can't Win" before Erica convinces him to drop it. that looks more like a Ruger speed 6 revolver
Beretta Px4 Storm
Hobbes uses a Beretta Px4 in "Red Sky" after he meets Marcus in a deserted parking lot.
Submachine Guns
Heckler & Koch MP5A3
A Heckler & Koch MP5A3 with a Surefire flashlight grip was seen in the Pilot in the hands of an anti-V resistance fighter. SWAT operators are also armed with the MP5A3 in numerous episodes. In the Season 2 episode "Siege", an MP5A3 with a UMP stock, RAS forearm, and ACOG scope was used by one SWAT operator (this appears to be the exact same prop used in several episodes of Human Target, which had the same armorers as this show).
FN P90
One of Eli Cohn's (Oded Fehr) Fifth Column members used an FN P90 with a tactical light in the Season 2 episode "Siege".
Assault Rifles
M4A1
M4A1 carbines are carried by National Guardsman in their New York deployment in the Pilot episode. However, they should be armed with the M16A2 as it is their standard rifle. M4A1 carbines have been making a regular appearance throughout both Seasons 1 and 2 in the hands of NYPD SWAT officers and FBI hostage rescue agents. Several M4A1 carbines were also seen in the hands of Project Ares sentries when Lars Tremont (Marc Singer) brought Erica Evans into the situation room of the Project Ares bunker in the Season 2 episode "Mother's Day".
Heckler & Koch G36C
A Heckler & Koch G36C was seen with a few other firearms on the desk of Kyle Hobbes (Charles Mesure) in the Season 2 episode "Red Rain".
SIG SG 552
SIG SG 552 compact assault rifles were seen in the hands of Eli Cohn's (Oded Fehr) Fifth Column members in the Season 2 episode "Siege".
Shotguns
Remington 870
A Remington 870 was used in the Pilot by an anti-V fighter. Never used, and also seen in "Heretic's Fork" held by Mrs. Thompson.
Sniper Rifles
Remington 700
A Remington 700 is wielded by John May (Michael Trucco) when he corners Ryan as an anti-Fifth Column soldier in "John May". Kyle Hobbes (Charles Mesure) also uses a Remington 700 rifle fitted with a Choate Ultimate Sniper rifle stock in "We Can't Win" to take down a sniper who shot Alex. Hobbes would use the same rifle again in the Season 2 episode "Concordia" where he used the rifle to shoot Marcus.
Unknown Rifle
Mr. Thompson is seen with an unknown bolt-action rifle in "Heretic's Fork". From a closer look at the bolt, it appears that the rifle is a sporterised Mauser 98 bolt-action rifle.
Others
FIM-43 Redeye
Kyle Hobbes (Charles Mesure) uses a FIM-43 Redeye mocked up as a FIM-92A Stinger in "Hearts and Minds" to take down a V shuttle used for military purposes, until he and the other Fifth Column fighters find out it was supposedly filled with human passengers. In order to more closely emulate the Stinger launcher, it is fitted with a fake IFF antenna made out of sheet metal, and is also fitted with a transparent face shield.