A likely stand-in for the Glock 22, FBI Special Agent Seeley Booth (David Boreanaz) is seen armed with a Glock 17 as his sidearm for the first two seasons, replacing the Smith & Wesson Model 686. For a few episodes, Booth's Glock is shown with a stainless slide.
Glock 19
During The Lance to the Heart when Booth (David Boreanaz) cleans a Beretta pistol, Glock 19 pistols obtained from the FBI armory are seen placed on a table.
Glock 23
In Season 4's "The Man in the Outhouse" (S4E03), a Glock 23 is taken as evidence. It is said to be .40 caliber, which combined with its compact size, narrow it down as a G23. FBI Special Agent Seeley Booth (David Boreanaz) is seen with the Glock as his service sidearm before being replaced by M1911 variant pistols.
M1911 variant pistols
FBI Special Agent Seeley Booth (David Boreanaz) is seen with various M1911 pistols as his primary firearm in the series.
Colt MK IV Series 80 Enhanced Commander
In Season 5's premiere "Harbingers in the Fountain", what appears to be a Colt MK IV Series 80 Enhanced Commander is given to Booth by Sweets when Booth got reinstated into the FBI.
Smith & Wesson SW1911PD
In Season 4's "The Con Man in the Meth Lab" (S4E09), Booth is seen carrying a Smith & Wesson SW1911 PD Tactical Rail Series as his sidearm.
Replacing the GSR, Booth (David Boreanaz) is seen with a Smith & Wesson SW1911 with a stainless slide as his main weapon in Seasons 6, 7, and 9.
Beretta 92FS
Booth (David Boreanaz) is seen cleaning a Beretta 92FS obtained from the FBI armory during The Lance to the Heart.
Beretta 950 Jetfire
A compact pistol is used by a man to kill his dwarf brother in Season 5's "The Dwarf in the Dirt" (S5E07). It was initially identified as a Ruger MkIII, but upon closer inspection, the pistol appears to be a molded off Beretta 950 Jetfire.
Beretta U22 Neos
In Season 4's "The Beaver in the Otter" (S4E24), a Beretta U22 Neos is seen used at a rally and is a suspected murder weapon.
SIG-Sauer P226
Detective Jared Booth pulls a SIG-Sauer P226 in the Season 4 finale "The End in the Beginning" (S4E24).
SIG-Sauer P229
The SIG-Sauer P229 is carried by several FBI agents in the series. In Season 1's "Two Bodies in the Lab", Special Agent James Kenton (Adam Baldwin) carries the SIG and it's also handled by Brennan in the episode.
SIG-Sauer P239
Detective Camille Saroyan (Tamara Taylor) draws a SIG-Sauer P239 in the Season 4 finale "The End in the Beginning" (S4E24).
Smith & Wesson M&P
The Smith & Wesson M&P pistol is carried by Dr. Lance Sweets (John Francis Daley) and Special Agent James Aubrey (John Boyd).
Tokarev TT-33
In Season 6's "The Mastodon in the Room" (S6E01), an insurgent uses a Tokarev TT-33 to hold a young boy hostage.
Walther PPK
In Season 5's "The Bond in the Boot" (S5E2), a suppressed Walther PPK is used by a CIA field operative to kill a Russian diamond courier. The weapon is also used by Special Agent Booth (David Boreanaz) in London.
Revolvers
Smith & Wesson Model 500
In Season 2's "The Man in the Cell" (S2E12), Dr. Temperance "Bones" Brennan (Emily Deschanel) begins carrying a 4" Smith & Wesson Model 500 that she claims to have bought at the mall. The impracticality of the large-caliber gun for the purposes of law enforcement becomes a running gag in the series. She and Booth both use the weapon in the final showdown with a murderer in Season 3's "Mummy in the Maze" (S3E05). The killer mentions in the episode that the .500 caliber 500 only holds 5 shots, and Booth takes advantage of its power to shoot through a metal door.
Smith & Wesson Model 625
In the pilot episode, Dr. Temperance "Bones" Brennan (Emily Deschanel) uses what appears to be a Smith & Wesson Model 625 at an indoor shooting range and what may be the Non Guns model is used to wound a suspect in the leg.
Smith & Wesson Model 686
In the initial episodes of Season 1, Booth carries a Smith & Wesson Model 686 as his sidearm. In Season 4's "The Con Man in the Meth Lab" (S4E09), Sheriff Leonard Wilkinson (Brian Howe) appears to use this revolver to hold a woman hostage.
In Season 6's "The Sin in the Sisterhood" (S6E12), a farmer is shown to possess an early snub-nosed Smith & Wesson Model 10 for protection. Camille Saroyan (Tamara Taylor) is later seen shooting it (to "relive stress") into ballistic gel.
Smith & Wesson Model 19
A Smith & Wesson Model 19 is seen in the hands of a murder victim in Season 3's "Soccer Mom in the Mini-Van" (S3E02).
Shotguns
Mossberg 590 Cruiser
In Season 6's "The Body and the Bounty", a bounty hunter is seen using a Mossberg 590 Cruiser to fire beanbag rounds. Brennan is also seen holding the Mossberg.
Mossberg 590 Special
In Season 1's "Two Bodies in the Lab", FBI agents are armed with Mossberg 590 shotguns during a raid on a warehouse.
Remington 870 MCS
In Season 4's "The Man in the Meth Lab" (S4E09), Booth holds a Remington 870 Tactical shotgun on a suspect.
Remington 870 Police
A Remington 870 Police model with a dedicated forend weaponlight is carried by Booth when he accompanies an FBI SWAT team in Season 3's "The Pain in the Heart" (S3E15).
12 Gauge Sawed-off Double Barreled shotgun
In Season 3's "Mummy in the Maze", the murderer dressed as a clown uses a sawed-off 12 Gauge Double Barreled Shotgun in a shootout with Booth. Booth mentions how a military man can miss with a scattergun.
Double Barrel Shotgun
In Season 5's "The X in the File" (S5E11), a female rancher holds a 12 Gauge Double Barreled Shotgun loaded with rock salt to shoo people off her land.
Rifles/Carbines
AKM
The AKM is used by an insurgent in Season 1's "The Soldier on the Grave" (S1E21).
FN SCAR-L
An FN SCAR-L is used by Jacob Broadsky (Arnold Vosloo) in Season 6's "The Hole in the Heart".
M4A1 Carbine
The M4A1 is seen carried by US Army troops in Season 1's "The Soldier on the Grave" (S1E21). FBI SWAT is seen armed with the M4A1 in Season 3's "The Pain in the Heart". Booth is seen carrying and firing an M4A1 with a Laser aiming module, weaponlight and foregrip in Afghanistan in Season 6's "The Mastodon in the Room" (S6E01).
M-1A
A M-1A with Sage Stock is used by a US Army soldier in Season 1's "The Soldier on the Grave" (S1E21).
M1 Garand
An U.S Army honor guard is shown with M1 Garand rifles in both Season 1's "The Soldier on the Grave" (S1E21) and when Booth is seen as part of another honor guard.
Winchester Model 1892
In Season 4's "The Princess & The Pear", a Winchester Model 1892 is seen hanging on Booth's mantle in his apartment.
A Barrett M107CQ is seen in the hands of Jacob Broadsky (Arnold Vosloo) in Season 6's "The Killer in the Crosshairs" (S6E21).
Remington Model 700P LTR
In Season 6's "The Bullet in the Brain" (S6E11), Agent Booth takes his Remington 700P LTR sniper rifle to see how did Broadsky took a shot from such distance (1400 m) to kill "The Gravedigger"/Heather Taffet (Deidre Lovejoy). It was stated earlier in the episode that the caliber of the bullet was a .338 Lapua Magnum, which is assumed to be a stolen Barrett M98 Bravo from Leishenger. Also in Season 6's "The Killer in the Crosshairs" (S6E21), Booth uses his own M700 that he kept in his car to shoot Broadsky's rifle in order to prevent the death of a dirty cop.
Winchester Model 70
In Season 5's "The Boy With The Answer", Max Keenan (Ryan O'Neal) uses what appears to be a Winchester Model 70 in an attempt to murder Heather Taffet (the Gravedigger).
Booth and FBI HRT agents are armed with the Heckler & Koch MP5A2 with SureFire dedicated forend weaponlights when raiding a hideout in Season 1's "The Woman in the Car".
M1928 Thompson
In Season 6's "The Bikini in the Soup", both Booth and Brennan are seen firing M1928 Thompson submachine guns to celebrate Valentine's Day.
Machine Guns
Browning M2
A Browning M2 HB is briefly seen mounted on top of a humvee in Season 1's "The Soldier on the Grave" (S1E21).
FN M249 SAW
The FN M249 SAW is held by US troops in Season 1's "The Soldier on the Grave" (S1E21).
Other
RM Equipment M203PI
In Season 4's "The Man in the Meth Lab" (S4E09), a police instructor shows recruits how to use a stand alone RM Equipment M203PI, which he fires into a broken down trailer. A body then erupts from the explosion and the episode's case begins.