In "The Cost of Living" (S05E05), Diakos (Adoni Maropis) uses what appears to be a Beretta 92FS when he assaults Stella. The gun is refered to as a "high caliber automatic pistol".
In "No Good Deed" (S05E16), a suspect drops a Beretta 92FS when being detained by Mac.
Beretta 92SB
In "Point of No Return" (S05E18), Dr. Marty Pino (Jonah Lotan) uses an unknown pistol that appears to be a nickel-plated Beretta 92SB (due to the rounded trigger guard).
Desert Eagle
In "Turbulence" (S5E03), Flack finds a Desert Eagle with pearl grips in a hotel room where an Air Marshal was murdered, the suspect apparently used a stuffed animal to suppress the sound of the gunshot.
In "Pay Up" (S5E25), a Desert Eagle is used by a kidnapper to kill Det. Jessica Angell. The kidnapper is seen using it in the climax of the episode, dropping it after being wounded by Flack. Hawkes is also seen holding one while he and Det. Monroe examine the .50AE round discovered at the crime scene.
Colt M1991A1
In "Veritas" (S05E01), a plain clothed NYPD officer is seen drawing an Colt M1991A1 when arresting Joe (Elias Koteas).
Kahr K9
In "My Name Is Mac Taylor" (S05E08), David Oka (Kelvin Yu) is seen with what appears to be a Kahr K9.
Luger P08
In "Yahrezit" (S05E22), a Neo-Nazi has several Luger P08 pistols. Another Luger fitted with a bayonet on the barrel is used by an ex-Nazi named Klaus Braun (Ed Asner) to commit a murder. The round doesn't penetrate deeply due to the gunpowder having degraded over the years.
Mauser C96
In "Yahrezit" (S05E22), a German SS officer is seen using a Mauser C96 to execute Jewish prisoners during a flashback.
Mauser 1910 Pocket Pistol
In "Communication Breakdown" (S05E19), what appears to be a Mauser 1910 Pocket Pistol is used by a father to ward off the man sleeping with his daughter. When the gun accidentally discharges it strikes a man on a passing train. The gun is misidentified as a .25 caliber.
SIG-Sauer P229
In "Turbulence" (S05E03), an air marshal's SIG-Sauer P229 is found by Adam, identified as a "Sig". The SIG is later seen in a flashback when James Turner (Scott Connors) holds the gun on a flight attendant.
SIG-Sauer P226
In "She's Not There" (S05E14), an ESU officer is seen with a SIG-Sauer P226 in preparation for a raid on a warehouse.
Taurus PT100
In "Pay Up" (S05E25), Terrence Davis (Nelly) is seen pulling a highly customized Taurus PT100.
Taurus PT911
In "Greater Good" (S05E23), hitman Ronnie DeSoto (Geoff Meed) is seen with a Taurus PT911.
Walther P38
In "Yahrezit" (S05E22), a Neo-Nazi is found in poseession of a Walther P38 along with his Lugers. Adam is later seen testing the weapon to match it against the murder weapon.
In "The Past, Present and Murder" (S05E21), a Smith & Wesson Model 65 is found in Dunbrook's (Craig T. Nelson) office. It is identified as a "Smith & Wesson .38 Special" and is seen being test fired by Stella in the lab.
Submachine Gun
Heckler & Koch MP5A2
In "Veritas" (S05E01), plain clothed NYPD officers are seen with Heckler & Koch MP5A2s.
In "Turbulence" (S05E03), ESU officers are seen with Heckler & Koch MP5A2s while the CSIs investigate the murder aboard an airplane.
Heckler & Koch MP5A3
In "Veritas" (S05E01), a plain clothed NYPD officer is seen with a Heckler & Koch MP5A2.
MP40
In "Yahrezit" (S05E22), during a flashback, German SS officers are seen with MP40s.
Assault Rifles
AKMSU
In "Point of No Return" (S05E18), Little Stevie (Emilio Rivera) fires what appears to be an AKMSU at Danny, Flack and Mac.
Machine Guns
In "Yahrezit" (S05E22), an MG42 is seen in the hideout of a Neo-Nazi.
Other
Pen Gun
In "The Cost of Living" (S05E05), a custom pen gun which fires a "rimfire .22 caliber" used by the real James Sutton (Chad Faust). It is seen being reconstructed by Sheldon and Mac.
Taser
In "Enough" (S05E06), Det. Stella Bonasera (Melina Kanakaredes) uses a taser which resembles a modified Remington 870 and is also similar to the Taser X12. It fires what Stella identifies as a "wireless charge with 4 barbs that packs a 1500 volt punch for up to 20 seconds." (In reality, this type of modified Remington is used by police departments to fire beanbag rounds.)
Unknown Launcher
In "Page Turner" (S05E02), officers in riot gear fire what are described by Det. Flack as "37mm soft rounds, bean bags" from an unknown launcher. It looks like a DefTech 37mm launcher but the tubes are not as long as tehy are on the DefTech.