The following weapons were used in the film Zodiac:
The Zodiac killer uses, as he tells the police in a phone call, a "Nine millimeter Luger" during his opening shooting of Darlene Ferrin and Mike Mageau in Vallejo on July 4, 1969. Later, Toschi finds a 9 mm Luger casing at the scene of the cab driver's murder. This was the same sort of pistol he had used during the actual killings as well.
During his Lake Berryessa stabbings of Bryan Hartnell and Cecilia Shepard, the Zodiac killer holds a M1911A1 on them. When Bryan asks if the gun was loaded, the Zodiac removes the magazine to show him the .45 rounds inside.
Ruger Mk I Pistol
Armstrong finds a ".22 automatic" inside Arthur Leigh Allen's house. It is described in dialogue as a '22 automatic' and it looks very much like a Ruger Mk I (aka the Standard, since the Mk I target had a longer barrel).
Colt Detective Special
San Francisco Inspector Dave Toschi (Mark Ruffalo) carries a snubnose revolver in his shoulder holster, never drawing it throughout the course of the film. It appears to be a Colt Detective Special based on the wooden grips. The grips are the design that were put on the 3rd generation Detective Special. In the movie it is also said that Toschi was the inspiration to the way Bullitt wears his gun in a shoulder holster.
Colt Official Police
After the Zodiac killer threatens his life, San Francisco Chronicle journalist Paul Avery (Robert Downey Jr.) asks Inspector Toschi for a gun and is subsequently seen firing off rounds from a Colt Official Police at a gun range. In real life, Avery was known to begin carrying a .38 revolver after he was threatened by the Zodiac.
Smith & Wesson Model 10
San Francisco Inspector Bill Armstrong (Anthony Edwards) keeps a Smith & Wesson Model 10 as his sidearm in a holster and, like his partner Toschi, never draws it throughout the film. In reality, the Colt Trooper was the standard issued sidearm for the SFPD during the 1970s.
Harrington & Richardson Model 949
Armstrong finds a ".22 revolver" inside Arthur Leigh Allen's house. Based on shape of frame, grip and barrel, it resembles a .22 LR H&R Model 949. H&R Model 949s were built from 1961 to 1972 and were inexpensive 22 revolvers.
Toschi finds an M1 Garand inside Arthur Leigh Allen's closet.