Also seen in use by Lex Luther (Michael Rosenbaum), also seen switched hands and used by Lana Lang (Kristin Kreuk) once to shoot open Lex's suitcase. Security, cops, and guards also seen in use. In season 7, Lex was seen duel wielding these. In fact, this is the most commonly seen weapon in the entire series, usually in the hands of Lex. In season 4 we see a suppressed one, also taken by Lex from his wouldbe assassin.
Beretta 92FS
Gabriel Duncan (Johnny Lewis) uses a Beretta 92FS to kill the guards in the missile silo, and to shoot and kill Clark Kent (Tom Welling). Clark was later shot with it by Chloe Sullivan (Allison Mack). It appears to be a non-gun, as it doesn't cycle when it fires.
SIG-Sauer P226
In the season 4 episode "Onyx", Evil Lex uses a stainless SIG-Sauer P226.
Smith & Wesson Model 610
A Smith & Wesson Model 610 is a prop gun used in the episode as a prop gun for a movie made. It was decorated as a villain weapon. Season 7, episode 5 "Action". This is most likely the same revolver that we saw Blade used briefly in Blade Trinity.
Smith & Wesson Model 60
Pete Ross (Sam Jone III) in one of the early seasons used a Smith & Wesson Model 60 stub nose revolver.
Heckler & Koch G36C
What appears to be a Heckler & Koch G36C with a modified scope and laser sight is used in the season three episode "Extinction" by the character Van McNulty (Jesse Metcalf).
Heckler & Koch MP5A3
Seen used by security guards employed by Lex. These have retractable buttstocks.
MacMillan TAC-50
Seen in Season 5, episode titled Fanatic by some stalker, psycho girl and then made Lois Lane use it.
M16
Used by Whitney Fordman while serving as a Marine in Indonesia.
Also used by National Gaurd troops in the season 4 finale
Winchester Model 1873
Seen used by Clark's adopted dad, who somehow managed to sneak it past a billionaires security team
The Glock 17 is used by police officers and other characters in the series. Also the Glock featured is a second generation Glock, giveaways being the finger grooves and tactical rail are absent.
H&K MP7A1
Desert Eagle
Modified to fire tranquilizer darts
M4A1
Used by the army while searching nuclear missile silos for Gabriel Duncan.
Mini Uzi
A Mini Uzi is used by Lex Luther (Michael Rosenbaum) when under the control of Bob Rickman (Rick Peters).
Mossberg 930
A Mossberg 930 is used by Jonathan Kent (John Schneider) when under the control of Bob Rickman (Rick Peters).