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" (S5E02), 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.
Shotguns
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
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.