The Kimber Warrior was the sidearm of choice for Jonas Blane throughout Season 4 (and occasionally in earlier seasons), replacing the Custom TLE II.
Colt M1911A1
The M1911A1 is a frequent weapon seen in the series. Master Sgt. Mack Gerhardt (Max Martini) carries one as his sidearm. An M1911A1 with a suppressor and night vision scope was used by Bob in Season 4's "Dancing Lessons". Another scoped 1911 (likely the same prop weapon) was used by one of the terrorists who tries to kill Jonas when he rescues Molly in "Endgame".
SIG-Sauer P225
The SIG-Sauer P225 is used by Sgt. Charles Grey (Michael Irby) with a suppressor in Season 4's "The Last Nazi" (S4E14). SSgt. Sam McBride (Wes Chatham) is seen with a P225 in the opening scene of Season 4's "Hero".
SIG-Sauer P226
The SIG-Sauer P226 is the sidearm of Sgt. Charles Grey (Michael Irby) and Sgt. Hector Williams (Demore Barnes) throughout the series. Master Sgt. Mack Gerhardt (Max Martini) uses a P226 throughout Season 1 before switching to his M1911A1. P226s are used by a number of Leon Drake's men (including Drake himself) with and without suppressors throughout Season 4.
SIG-Sauer P229
The SIG-Sauer P229 is a commonly featured handgun throughout the series. US Army intelligence officer Bridget Sullivan (Nicole Steinwedell) uses a two-tone P229 in the Season 4 premiere "Sacrifice" (S4E01). Mack mentions that she carries a .45, which is incorrect, as the P229 is only chambered in 9mm, .40S&W, and .357 SIG). Bridget's P229 is briefly seen again in "Best Laid Plans". Similar weapons (likely the same prop guns) are used by the female kidnapper in "Dancing Lessons", and the assassin in "The Last Nazi".
SIG-Sauer P230
A suppressed SIG-Sauer P230 was used by one of the Russians who ambushes Bob in Season 4's "Endgame".
Glock 17
The Glock 17 is one of the weapons prominently featured throughout the series. Charles Grey (Michael Irby) uses a Glock 17 during the opening scene of "Sacrifice".
Glock 19
The Glock 19 is also used by numerous characters throughout Season 4. President-elect Benjamin Castillo (Benito Martinez) is seen with a Glock when he is confronted by the team in Season 4's "Sacrifice". They are used frequently by terrorists in other episodes, including "Switchblade", "Inquisition", and "Dancing Lessons".
Glock 26
A Glock 26 is briefly seen among other handguns when Sam (Wes Chatham) is choosing his sidearm. He initially selects the G26 but is convinced otherwise by Mack and takes a USP .45 instead.
Beretta 92FS
The Beretta 92FS has been seen in the hands of SWAT members, Unit members, and US military CID agents. Sam McBride (Wes Chatham) takes a 92FS from a police officer in "Whiplash" (S4E19).
In "Sex Trade" (S4E03), Bridget takes a Heckler & Koch P7 off a dead terrorist.
Cobra Big Bore Derringer
In Season 4's premiere "Sacrifice" (S4E01), Army intelligence officer Bridget Sullivan (Nicole Steinwedell) carries a chrome plated Cobra Big Bore Derringer as a backup that she has to use when engaging a terrorist disguised as a National Guardsman.
Norinco Model 54
Norinco Model 54 pistols were used by Chinese officers in Season 4.
Kahr K9 M9098 Elite
In Season 4's "Sudden Flight" (S4E2), the head terrorist uses a Kahr K9.
Makarov PM
The team finds a Makarov PM on a deceased Spetznaz member in Season 4's "Chaos Theory", and identified by Bob as "Kirovsky(?) 9mm armor-piercing Standard Spetznaz Issue". In all likelihood, this is meant to stand in for an SR-1 Gyurza, though it is clearly a Makarov, with the grips being the most obvious giveaway. There is a noticeable goof when the team finds the weapon: in the initial shot of the stairway the Makarov is gone, it only appears during the close up shot. Other Makarovs are seen throughout the episode. O
Smith & Wesson 6904
A Smith & Wesson 6904 is among the handguns seen in the gun drawer when Sam selects his sidearm in Season 4's "Hero".
Smith & Wesson SW99
In Season 4's "Best Laid Plans", one of the men employed by Leon Drake (David Rees Snell) tries to use his S&W Model 99, but it doesn't fire.
Jericho 941 R
In Season 4's "Flesh & Blood", Joss' bodyguard carries a reverse two-tone Jericho 941 R, which he expertly relieved of by Grey.
Revolvers
Colt New Service
A Colt New Service is seen when Jonas searches Sam's storage unit in Season 4's "Whiplash".
Webley Mk IV
A Webley Mk IV is seen in the hands of a tribal member is Season 4's "Shadow Riders"
Smith & Wesson Model 36
In Season 4's "Sex Trade", a Smith & Wesson Model 36 is planted on a male student who tried to blackmail Tiffy.
Smith & Wesson Model 60
A Smith & Wesson Model 60 was seen in the Season 4 premiere "Sacrifice" as Mack's throw away gun.
Colt Single Action Army
In Season 4's "Switchblade", Grey is seen restoring a classic Single Action Army.
Submachine Guns
Heckler & Koch MP5A3
The Heckler & Koch MP5A3 is used throughout Season 4. In "The Last Nazi" (S4E14), a bodyguard carries a Heckler & Koch MP5A3 equipped with a tri-rail, Aimpoint red dot sight, and vertical foregrip.
Heckler & Koch MP5SD3
Heckler & Koch MP5SD3s are seen used by the Unit in Season 4's premiere "Sacrifice" (S4E01). Strangely, in season 4, the sound effects used are those of unsuppressed weapons.
Heckler & Koch MP5K
In "Sacrifice" (S4E01), Jonas, Mack and Hector are all seen using Heckler & Koch MP5K submachine guns in the series. Jonas and Mack were seen using the newer Navy trigger group variant, while Hector was seen using one with the old "SEF" trigger.
A Mexican Special Forces member is briefly seen holding a Heckler & Koch UMP when taking orders from Mack in "Sudden Flight" (S4E02).
Uzi
A full size Uzi was used by terrorists as well as Grey in Season 4.
Mini Uzi
A Mini-Uzi is used by Bob in "The Conduit" (S4E04).
Micro Uzi
A Micro-Uzi is used by a terrorist in the series finale "Unknown Soldier" (S4E22).
Škorpion vz. 61
The Škorpion vz. 61 was used by hijackers in "Sudden Flight" (S4E02).
Rifles/Carbines
Colt M4A1 Carbine
M4A1 Carbines are used by all members of the Unit, often with a 40mm M203 Grenade Launcher, and with an optical sight (normally the Trijicon ACOG, Aimpoint CompM2 and/or EOTech 552 Holographic sight).
Heckler & Koch HK416
Colonel Ryan uses a Heckler & Koch HK416 in Season 4's "Into Hell Part 1", though it is very difficult to identify clearly (the DVD extras provide a better view, albeit briefly).
Mark 18 Mod 0
Grey wields a custom built Mark 18 Mod 0 rifle in the opening scene of "Hero" (S4E15). It appears to be the same weapon used by Jack Bauer in Season 7 of 24. Despite being equipped with a red dot sight and magnifier, the reticle shown is that of a normal rifle scope.
Heckler & Koch G3
Heckler & Koch G3 rifles are used by rebel forces aiding the Unit in "Flesh & Blood" (S4E17).
Galil ARM
One of the guards fires at the Unit with a Galil ARM in "The Conduit" (S4E04).
Marlin Model 336
The Park Ranger who gets shot in the Season 4 premiere "Sacrifice" (S4E01) was seen with a Marlin Model 336. Bridget is seen putting the rifle on the Ranger to distract the terrorist shooting at her. Another is seen in Carson's truck in "Switchblade."
Kentucky Flintlock Rifle
In Season 4's premiere "Sacrifice" (S4E01) , Grey finds a Kentucky Flintlock Rifle in the cabin when they prepare to make their last stand. They don't fire it, but they use the black powder to make an improvised explosive.
Shotguns
Remington 870 Wingmaster
Mack used a vintage Remington 870 shotgun while posing as a bird hunter in "Sacrifice" (S4E01).
Machine Guns
Browning M2 Aircraft
A Browning M2 Aircraft model is seen used as a doorgun on the UH-1 Huey sent to extract the Unit in Season 4's "Into Hell, Part 2" and again in "The Spear of Destiny".
RPD
In Season 4's "Into Hell, Part I", one of the sentries that confront the Unit at the Syrian border is seen handling an RPD machine gun.
M60
An M60 machine gun is seen in the arms cache found by Bob Brown and Dr. Donald Metz (Michael McKean) in Season 4's "Switchblade".
M60E4/Mk.43 mod. 1
An M60E4/Mk.43 mod. 1 MG was used by Jonas briefly in "Into Hell, Part I" (S4E07). The E4's distinctive picatinny rails on the receiver cover and forend, and the removable front grip are visible on Jonas' weapon.
DShKM Heavy Machine Gun (Browning M2 mockup)
A Browning M2 mocked up to resemble the DShK heavy machine gun is frequently used in the series. The machine gun was set up by Syrian forces in Season 4's "Into Hell, Part II" and fired by Mack in Season 4's "Switchblade".
Sniper Rifles
Remington 700 AICS
A sniper rifle frequently used by The Unit is a Remington 700 AICS. Mack also used this in Season 4's premiere "Sacrifice" and again in "Endgame". Sam McBride (Wes Chatham) is seen with this rifle in Season 4's "Best Laid Plans" (fitted with a Elcan Digital Day/Night scope, which is inaccurately portrayed not only as being a thermal scope, but as being able to detect heat through windows and curtains) and again in "Whiplash". The action is a Remington variant since the bolt is not an AI design. The folding stock hinge and adjustable cheek piece are visible in the close-up, so this would be an AICS 2.0 model. Also, AI L115 rifles are generally outfitted with Schmidt and Bender PMII scopes which this scope is definitely not. Also, unless the magazine has been removed (unlikely during a mission), the magazine on an actual Accuracy International AW/M will be protruding from the bottom of the stock. Visible is the paddle style magazine release in front of the trigger guard which would normally be blocked by an inserted magazine. This rifle is the same rifle used by Micheal Weston in season 2 of Burn Notice. The giveaway is the scope rings are the same cheapies seen on Jonas' rifle here. They should be heavy badgers or warnes.
In Season 4's "Best Laid Plans", Bob Brown (Scott Foley) is seen with a Gen 2 AIG Asymmetric Warrior ASW338LM modular sniper rifle in .338 Lapua Magnum while covering Jonas and Mack. Bob uses this rifle again during the standoff with Sam in "Whiplash".
Heavy Weapons
Cobray CM203 37mm Flare Launcher
M4A1 carbines fitted with the Cobray CM203 37mm Flare Launcher standing in for the M203 were used by Bob, Grey, and Mack on the mission to Iraq to rescue Betsy Blane in "Into Hell: Part 1" (S4E07) and "Into Hell: Part 2" (S4E08).
Other
M67 "Baseball" Grenade
The M67 "Baseball" Grenade is used throughout the series. In "Whiplash" (S4E19), Sam booby traps the door to the office he barricades himself in with three M67s.
M26 "Lemon" Grenade
A terrorist attempts to use an M26 hand grenade before being shot in "Hill 60" (S4E16). Jonas finds a crate of them in Sam's storage locker. Sam later uses one to aid his escape, though strangely when he barricades himself in the auto dealership office, he is shown to have booby trapped the door with M67 grenades.
CTS Model 7290M Mini Bang
A CTS "Mini Bang" is used by Jonas (combined with some drugs and chemicals found in the lab) in "Mislead and Misguided" (S4E10). During the standoff in "Whiplash" (S4E19), Sam holds one up to the window, calling it a concussion grenade. It should be noted that, though flashbangs are often erroneously called concussion grenades, the two are very different, as concussion grenades are much more deadly then flashbangs. Given the dialog of the scene, it's likely that the filmmakers intended for this to be an actual concussion grenade, and simply used a prop flashbang during filming.
"ALS" prop Flashbang
Sam McBride uses an unknown Flashbang in the opening scene of "Hero" (S4E15). These grenades bear the logo of ALS Technologies (a real company which actually makes stun grenades), however they look nothing like any product in ALS's catalog. These are likely prop replicas.
Crossman Air Pistol
Two Crossman air pistols loaded with tranquilizers were used by Afghan Tribesmen to incapacitate Jonas and Mack in Season 4's "Shadow Riders."
Wheelie bag carrying handle gun
In "The Conduit" (S4E04), Bob and Jonas had these weapons disguised as the carrying handles for their wheelie bags. It appears each of the square extendable rods were hidden barrels that each load one round, possible .22 or something small. To fire, they collapse the carrying handle forward into the smaller rod like you would a carrying handle of this type and it fires both rounds at the same time. I don't know if this is a real firearm, but it acts like one. Meant to be used to disarm armed men with real guns.
Gun Racks
When Grey is taken to Carson's house in Season 4's "Switchblade," a gun rack with unknown rifles on it is seen briefly. Two others are seen in the hardware store in Season 2's "Manhunt."