FBI Special Agent Seeley Booth (David Boreanaz) carries a Glock 17 as his sidearm for the first two seasons. For a few episodes, starting with Season 1's "The Man On The Fairway", Booth's Glock is shown with a stainless slide.
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.
Smith & Wesson 1911PD
In Season 4's "The Con Man in the Meth Lab" (S4E09), Brennan takes a Smith & Wesson SW1911PD Tactical Rail Series out of Booth's holster. It has a tactical rail on the frame nose.
Compact 1911 Variant
In Season 5's premiere "Harbingers in the Fountain", a compact M1911 variant is given to Booth by Sweets when Booth got reinstated into the FBI.
Seen in the season 4 finale. Used by Detective Jared Booth in the season 4 finale.
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).
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. Also used by agent Booth in London.
Beretta 21 Bobcat
A Beretta 21 Bobcat is used by a man to kill his dwarf brother in Season 5's "The Dwarf in the Dirt" (S5E7). It's called a Ruger MkIII but is a Beretta 21.
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.
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.
In Season 6's "The Sin in the Sisterhood" (S6E12), a farmer is shown to have a snub-nosed Smith & Wesson Model 10 for protection. Camille Saroyan (Tamara Taylor) is later seen shooting it (To "relive stress") into ballistic gel.
Shotguns
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 New Tactical
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
M4A1 Carbine
The M4A1 is seen carried by US Army troops in Season 1's "The Soldier on the Grave" (S1E21).
Booth is seen carrying and firing an M4 with a Laser aiming module, Red dot sight, surefire torch and a front grip in Afghanistan in episopde one of series six
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).
AKM
The AKM is used by an insurgent 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.
Remington Model 700
In Season 6's "The Bullet in the Brain" (S6E11), Agent Booth & Dr. Brennan find a Remington 700 sniper rifle that was used to assassinate "the Gravedigger" (Deirdre Lovejoy). It was stated earlier in the episode that the caliber of the bullet was a .338 Lapua Magnum.
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.
Remington 700
In Season 5's "The Boy With The Answer", Max Keenan (Ryan O'Neal) uses what appears to be a Remington 700 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".
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
M203 grenade launcher
In Season 4's "The Man in the Meth Lab" (S4E09), a police instructor shows recruits how to use a stand alone M203 grenade launcher, which he fires into a broken down trailer. A body then erupts from the explosion and the episode's case begins.