FBI Special Agent Seeley Booth (David Boreanaz) carries a Glock 17 as his sidearm on the show. 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 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 "Sin in Sister Hood" A farmer owns a snub-nosed version of the Model 10 for Protection and Cam is later seen shooting it (To "relive stress") into gel.
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 .50 caliber 500 only holds 5 shots, and Booth takes advantage of its power to shoot through a metal door.
Smith & Wesson 1911
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
Seen in the season 5 opener, given to Booth by Sweets when Booth got reissued into the FBI.
Seen in S5E2 used by a CIA field operative to kill a Russian diamond courier. Also used by agent Booth in London.
SIG-Sauer P226
Seen in the season 4 finale. Used by Detective Jared Booth in the season 4 finale.
SIG-Sauer P239
Detective Camille Saroyan (Tamara Taylor) draws a SIG-Sauer P239 in the Season 4 finale "The End in the Beginning" (S4E24).
Beretta 21 Bobcat
A Beretta 21 Bobcat is used by a man to kill his dwarf brother in Season 5x7. 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.
Shotguns
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 used by Booth in Season 1's "".
Sawn-off Double barrel shotgun
In Season 3's "Mummy in the Maze", the murderer dressed as a clown uses a sawn-off double barrel 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 rancher woman uses a Double Barrel 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".
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".
AKM
The AKM is used by an insurgent in Season 1's "The Soldier on the Grave".
M1 Garand
An U.S Army honor guard is shown with M1 Garand rifles in both Season 1's "The Soldier on the Grave" 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.
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".
FN M249 SAW
The FN M249 SAW is held by US troops in Season 1's "The Soldier on the Grave".
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.