Second generation Glock 17 pistols are used by the members of the FBI, most notably Charlie Francis (Kirk Acevedo). At the beginning of Season 1, Agent Dunham (Anna Torv)'s standard weapon is a Glock 17, with a Glock 26 as a BUG (as seen in episode 2). Midway through the season, she switches to the Glock 26 full-time.
Glock 19
A Glock 19 is Phillip Broyles (Lance Reddick) sidearm, although he rarely uses it. It is also seen very briefly in the hands of NYPD in one episode, and by Mitchell Lobe (Chance Kelly) before he is disarmed and taken into custody.
Glock 26
Olivia Dunham's (Anna Torv) sidearm is a sub-compact Glock 26, 9mm. The same sidearm is also used by Nick Lane, who was part of the same program as Dunham, likely prompting use of the same firearm. Agent Dunham's Glock 26 is borrowed once by Peter Bishop, who doesn't carry a gun himself.
SIG-Sauer P229R
A two tone SIG P229 with accessory rails and a suppressor is used in the attempted assassination of Nina.
SIG-Sauer P228
A SIG-Sauer P228 is seen used by both Olivia Dunham and John Scott in the Pilot. Peter Bishop buys and uses a SIG-Sauer P228 in S2E21.
Unknown Smith & Wesson Auto (1076?)
An unknown silver, DAO S&W Auto is seen in S1E9 "The Dreamscape" held by a man that Peter beats up. It looks like a S&W 1076, however the bore looks too small to be 10mm. (After doing some research it looks more like S&W .45 Auto)
Desert Eagle
A pair of .50AE Desert Eagles in chrome are requisitioned by Agent Dunham to kill the monster. Walter (John Noble) requests .50 caliber incendiary rounds in order to kill the creature, probably meaning a .50 caliber machine gun. Walter is surprisingly the one to kill the monster with two shots from his Desert Eagle. In the next shot, we can see that the gun has jammed after those two shots. A black Desert Eagle with a suppressor was also used by the assassin sent by the Observers in the episode "August" (S2Ep8).
Kahr K9
Mitchell Lobe (Chance Kelly) uses a black, suppressed Kahr K9 9mm to execute the member of his bank robbery team who gets stuck in the vault; the Kahr is never seen with the slide forward, even when "fired." Mitchell's wife Samantha (Trini Alvarado) retrieves his Kahr K9 in stainless from a closet in order to try to kill Agent Dunham. Mitchell seems to have a thing for the K9.
Smith & Wesson Model 10
The scientist who responds to the silent alarm at the genetics facility is armed with a Smith & Wesson Model 10. A S&W Model 10 HB is used by a store owner in S2Ep7.
Beretta 92FS
A Beretta 92FS was used by a guard at a cryogenics facility in S2Ep4 where it is used to kill a shape shifter. In S2Ep7 a teenage mind controller makes Peter steal a Beretta 92FS from a policeman, then makes him shoot Agent Broyles with it.
Beretta Cougar
Two of these are used by a shape shifter in S2Ep4 to kill the guards at a cryogenics facility. They appear to be Beretta Cougars. These are apparently standard equipment of guards for the mysterious antagonists in the show.
Colt M1911A1
An old-looking Colt M1911A1 is used by a young woman under psychic possession by a Navy Officer. She retrieves it from his house.
SIG-Sauer P239
In S1E3 "The Ghost Network" the assassin uses a SIG-Sauer P239 with a an Advanced Armament Corp. Black Box suppressor to kill Grant (Peter Hermann).
The Observer's Pistol
The Observer uses a pistol in S1E4 "The Arrival" to tranq Peter (Joshua Jackson). It looks a bit like a Walther PPK or a Detonics Pocket 9 in S2E8 "August" the Observer pistol is shown to also fire sonic shock wave like the minority report Sonic Gun. it implied that is a advance weapons because Phillip Broyles said that the tech's can't get it to work.
Walther P99
Used by Olivia in season 1 in the episode where she gets captured.
Heckler & Koch USP
Used by an F.B.I. Agent in season 1.
SIG-Sauer P226
All F.B.I. Agents who don't have actual roles appear to use SIG handguns.
Beretta Px4 Storm
A Beretta Px4 Storm is carried by agent Peter Bishop in year 2026, noticeably during his talk with "Walternate". we could assume that Beretta Px4 Storm is Fringe Division main side arm.
FN Five-seveN
The FN Five-seveN stands in as the futuristic sidearm of Fringe Division on the other side. It is referred to as the Model 76 handgun and was designed by William Bell. William Bell wields the 'Model 77' at one point which looks like it is merely another 5-7 with some different dress up components added to make it look different.
Vektor CP1
A black Vektor CP1 with a suppressor was used by a shape shifter In S3EP4
Battlestar Galactica sidearm
In the Season 2 Ep. 20 Brown Betty the Watcher hitmen (the Observers) carry what looks like the dressed up revolver used as the Colonial sidearm in the Battlestar Galactica mini-series.
Unknown revolver
in the S2E20 "Brown Betty" private eye Dunham carries a revolver going with the 1940 Noir look of Walters story in the episode. It looked a bit like a Ruger GP100, although you only see it once, in a bad angle.
Shotguns
Mossberg 500
A Mossberg 500 is seen in the car of the police officer who picks up Teddy in S2Ep12.
Winchester Model 1912
The Sheriff of Edina (Michael O'Neill) and his deputy carry Winchester Model 1912s in S2Ep12. They can be most easily identified by the large ejection port on the right side of the gun.
Unknown pump-action shotguns
In Season 2 Ep. 21 Northwest Passage Peter buys a shotgun when he believes the shapeshifters are after him.
Submachine Guns
Heckler & Koch MP5A3
FBI SWAT officers can be seen armed with Heckler & Koch MP5A3's with Navy trigger groups, some of them also having Surefire dedicated forend weaponlights in the pilot and S2Ep7.
Heckler & Koch MP5SD3
A Heckler & Koch MP5SD3 can briefly be seen being carried by one of the SWAT team members guarding the plane in the pilot episode (S01E01).
Jian She Type-05
Jian She Type-05 submachine guns are used by the hybrid shape shifters in "Enemy of My Enemy" (S04E09), and one is later picked up and used by Peter (Joshua Jackson).
Assault Rifles
M14 Rifle
A soldier in Iraq is seen with what looks like a M14 rifle fitted with an M68 Aimpoint Scope.
M16
A M16 rifle is seen carried by a guard at St. Claires mental institution.
M4 Carbine
SWAT team members are seen with M4 Carbine rifles as they debark their van before storming a suspected biological laboratory. Soldiers equipped with NBC equipment also have M4 Carbines when they quarantine a building in "What Lies Beneath."
Norinco QBZ-97B
Norinco QBZ-97Bs are carried by prime universe Fringe Division tactical teams in the year 2026.
=Sniper Rifles
Blaser R93 LRS2
What appears to be a Blaser R93 rifle is seen in a publicity photo of John Scott (Mark Valley).
Remington 700
A Remington 700 is seen in S2Ep7 and the pilot used by a SWAT snipers.
GALATZ - Galil Sniper Rifle
A Galil Sniper Rifle is used by alternate-universe Olivia to shoot down an enemy sniper in S4E17 (Everything in Its Right Place).
Machine Guns
M249 SAW
An American soldier in Bagdad is seen with what appears to be an M249.
Other Weapons
Shockwave Gun
In S1E4, a man looking for the cylinder uses a "Shockwave Gun" on multiple different people. It appears to be based on a real gun. Like an Mp5 or something similar.
Seems to be a Tippman A5 Paintball Marker w/ Eotech -Schiebi86
Tranquilizer Gun
Not seen clearly in an episode but seen in the special features for the episode where somebody teleports out of prison.