Torchwood agents Gwen Cooper (Eve Myles), Dr. Owen Harper (Burn Gorman), Ianto Jones (Gareth David-Lloyd) and Toshiko Sato (Naoko Mori) continue to carry the Tokyo Marui Hi Capa 4.3 (standing in for a real life compact M1911 variant). Various other characters are also seen with the weapon.
Beretta 92F/FS
In "Meat", Dr. Owen Harper (Burn Gorman) disarms one of the criminals of a Beretta 92FS. Another is later used by Dave (Marek Oravec) in the same episode.
An alien Blowfish (Paul Kasey) uses a stainless FN Model 1910 to take a family hostage in the Kiss Kiss, Bang Bang. He is killed by the recently returned Captain Jack Harkness (John Barrowman) before he can use it.
Remington 1866 Derringer
One of the firearms that Captain John Hart (James Marsters) hands over to Torchwood in "Kiss Kiss, Bang Bang" is a nickel plated Remington 1866 Derringer with pearl grips.
Heckler & Koch USP
In "Meat", Greg (Gerard Carey) is seen carrying a Heckler & Koch USP as his main weapon. In "Reset", a USP is wielded by Professor Aaron Copley (Alan Dale).
Revolvers
Webley Mk. IV
Captain Jack Harkness (John Barrowman) continues to carry a a Webley Mk IV in .38 as his primary weapon. Captain John Hart (James Marsters) briefly uses it in "Kiss Kiss, Bang Bang".
Smith & Wesson New Model No. 3
In "Fragments", a Smith & Wesson New Model No.3 is used by Torchwood operatives Alice Guppy (Amy Manson) and Emily Holroyd (Heather Craney) when torturing Jack to find out if the rumours about him being incapable of dying are true.
Submachine Guns
FN P90
Several FN P90 submachine guns fitted with sound suppressors can be seen in Torchwood Three's armory throughout the series.
Heckler & Koch MP5K-PDW
A pair of H&K MP5K-PDWs are used by Captain John Hart (James Marsters) during the Season 2 finale Exit Wounds. The folding stocks have been removed, however the PDW backplate is still present, as noted by the hinge that the stocks would normally attach to. Also present are the lugged barrels of the PDW variant, onto which the standard H&K flash-hiders have been attached.
Assault Rifles
Heckler & Koch G36C
The Heckler & Koch G36C is seen in the hands of UNIT soldiers in "Fragments".
Heckler & Koch G36KV
In "Sleeper", a British Army soldier is seem armed with a Heckler & Koch G36K. Although this is not accurate to real life (as the British Army uses the L85), it is consistent with the continuity of the parent show. Several G36KV's are also seen in the armoury of Torchwood Three throughout the series.
Mk 18 Mod 0
British Army soldiers guarding the nuclear stockpile in "Sleeper" are armed with Mk 18 Mod 0 carbines fitted with EOtech sights, foregrips, and tactical flashlights. The leader alien sleeper agent (Doug Rollins) briefly uses one to kill some of the soldiers.
Other
Captain John Hart Pistols
The pistols carried by Captain John Hart (James Marsters) in "Kiss Kiss Bang Bang" vaguely resemble a M1911 style handgun in a futuristic shell.
Torchwood Stun Pistol
In "Meat", Captain Jack Harkness (John Barrowman), Dr. Owen Harper (Burn Gorman), Gwen Cooper (Eve Myles) and Ianto Jones (Gareth David-Lloyd carry custom stun pistols as a non-lethal option. They have the Torchwood logo marked on the side.