Second generation Glock 17 pistols are used by the members of the FBI, most notably Charlie Francis (Kirk Acevedo).
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. 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 26
Olivia Dunham's (Anna Torv) sidearm is a sub-compact Glock 26, 9mm. The same sidearm is also used by Nick Lane, a man who is psychically linked to Agent Dunham causing him to have the same routines and habits, likely prompting use of the same firearm. Agent Dunham's Glock 26 is borrowed once by Peter Bishop, who doesn't routinely carry a gun himself.
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.
SIG-Sauer P239
In "The Ghost Network" (S01E03) the assassin uses a SIG-Sauer P239 with a an Advanced Armament Corp. Black Box suppressor to kill Grant (Peter Hermann).
Heckler & Koch USP
An F.B.I. Agent in "In Which We Meet Mr. Jones" (S01E07) uses a Heckler & Koch USP.
Walther PPK
Mitchell Lobe (Chance Kelly) can be seen with a Walther PPK in "The Equation (S01E08). A henchman in "The Transformation" (S02E13) also uses a PPK.
Smith & Wesson 1076
A S&W Automatic is seen in "The Dreamscape" (S01E09) being held by a man that Peter beats up. It is a compact size, double action only pistol with a stainless steel single stack frame meaning it is either a Smith & Wesson 1076, or possible a Smith & Wesson 4576.
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 in "Safe" (S01E10); 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 in "Bound" (S01E11). Mitchell seems to have a thing for the K9. A K9 is also carried by one of the weapons dealers in "The Transformation" (S01E13).
Walther P99
Agent Gunham picks up a Walther P99 whils escaping captivity in "Bound" (S01E11).
Beretta 92FS pistols can be seen in several episodes being used by police and bad guys alike.
Smith & Wesson Model 10
The scientist who responds to the silent alarm at the genetics facility in "Unleashed" (S01E16) is armed with a Smith & Wesson Model 10. A S&W Model 10 HB is used by a store owner in S2Ep7.
Desert Eagle Mark XIX
A pair of chrome plated .50AE Desert Eagle Mark XIX pistols are requisitioned by Agent Dunham to kill the monster in "Unleashed" (S01E16). 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).
Taurus PT92AFS
One of the henchmen in "The Road Not Taken" (S01E19) uses a Taurus PT92AFS
SIG-Sauer P229R
A two tone SIG P229R fitted with a suppressor is used in the attempted assassination of Nina Sharp in "The Road Not Taken" (S01E19).
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.
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.
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.
UTAS UTS-15
In "Letters of Transit" (S04E19), the Loyalist security forces can be seen using the UTAS UTS-15 pump action shotgun.
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
AKMS
A number of soldiers in Iraq carry what appear to be AKMS rifles in the pilot (S01E01).
M14 Rifle
A soldier in Iraq is seen with what looks like a M14 rifle fitted with an M68 Aimpoint Scope.
M16A4
A M16A4 rifles are seen on a number of occasions generally being carried by US soldiers.
Colt Law Enforcement Carbine
Colt Law Enforcement Carbine are frequently seen in the show being the mian weapon used by FBI HRT and Police SWAT teams.
Norinco QBZ-97B
Norinco QBZ-97Bs are carried by prime universe Fringe Division tactical teams in the year 2026.
Sniper Rifles
Remington 700
A Remington 700 is seen in S2Ep7 and the pilot used by a SWAT snipers.
Blaser R93 LRS2
John Scott (Mark Valley) can be seen with a Blaser R93 sniper rifle during a "memory" in "The Transformation" (S01E13).
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 in the pilot episode (S01E01).
Browning M2HB
A Browning M2HB can be seen mounted on the roof of a US Army Humvee in Baghdad in the pilot episode (S01E01).
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