DCI Ronnie Box (Simon Harrison) uses a Webley .38 Mk IV during the police operation in "Apollo" (S06E02). In "Confection" (S06E03) a pair of revolvers is found in the trunk of crashed car, one of them is a Webley .38 Mk IV. DS Endeavour Morse (Shaun Evans) and DI Fred Thursday (Roger Allam) use Webley .38 Mk IV revolvers in the climactic scene in "Degüello" (S06E04).
Smith & Wesson Model 10 HB
In "Confection" (S06E03) a pair of revolvers is found in the trunk of crashed car. One of them is a Smith & Wesson Model 10 HB.
Various revolvers
In the climactic scene in "Degüello" (S06E04) both DS Jim Strange (Sean Rigby) and Chief Superintendent Reginald Bright (Anton Lesser) draw revolvers but they are seen very briefly and unclear.
Pistols
Walther PPK
A Walther PPK is a murder weapon in "Apollo" (S06E02).
Browning Hi-Power
A Browning Hi-Power is one of the guns on film studio in "Apollo" (S06E02). In the climactic scene it is used by Hildegard Slayton (Mary Stockley). It is descrived as a live gun, used with blank ammo during filming.
Luger P08
A Luger P08 is one of the guns on film studio in "Apollo" (S06E02).
SIG P210
A SIG P210 is DCI Ronnie Box's (Simon Harrison) handgun in "Degüello" (S06E04). A firearms report incorrectly calls the pistol "SIG Sauer P210" instead of "SIG P210": the document is dated 1964 while SIG Sauer was formed only in 1976.
Makarov PM
A Makarov PM is DS Alan Jago's (Richard Riddell) handgun in "Degüello" (S06E04). The corrupt cop must have obtained this pistol, uncharacteristic for 1960s Britain, in some illegal way but still it's a strange choice of a gun.
Shotguns
Double Barrel Shotgun
Farmer Rennett Bell (uncredited) uses a Double Barreled Shotgun to murder his wife and then commit a suicide in "Confection" (S06E03).
Other Weapons
Captive Bolt Pistol
In "Confection" (S06E03) a captive bolt pistol is used by the veterinarian Charles Shepherd (Christopher Bowen) to put down a horse with broken leg. Same gun is later used by Isla Fairford (Olivia Chenery) to commit a murder.
Trivia
When DS Jim Strange examins firearms reports in archive in "Degüello" (S06E04), photos of a Mauser C96 and a SIG P210 (see above) are seen.
In same episode a photo of Eddie Nero's M1911A1 is seen in Strange's office (these events are described in "Icarus" (S05E06).)