A Glock 17 is carried by FBI Special Agent Dale Cooper (Kyle Maclachlan) in Season 3. He notably uses it in "Part 18" (S3E18) when confronting three men in a diner.
Glock 17 (Full Auto)
The Polish Accountant (Jonny Coyne) pulls a Glock 17 converted to full auto and loaded with a 33 round extended magazine to fire at a fleeing van in "Part 16" (S3E16).
Glock 26 (Two-Tone)
One of the men that confronts Agent Cooper in the diner (Matt Battaglia credited as "Cowboy 3") is forced to give up what appears to be a two-tone Glock 26 in "Part 18" (S3E18). Later disarming him, Cooper tosses it into a diner's deep fryer.
Colt MK IV Series 70
A stainless steel or nickel plated Colt MK IV Series 70 appears to be the sidearm of FBI Special Agent Albert Rosenfield (Miguel Ferrer), who pulls it in "Part 16" (S3E16).
Beretta 8000 Cougar
One of the men that confronts Agent Cooper in the diner (Rob Mars, credited as "Cowboy 2") is armed with a Beretta 8000 Cougar pistol. Later disarming him, Cooper tosses it into a diner's deep fryer.
Jericho 941 F
Cooper's doppelgänger (also Kyle Maclachlan) pulls what appears to be a two-tone Jericho 941 F in "Part 17" (S3E17).
The Walther P99 appears to be the sidearm of FBI Special Agent Tammy Preston (Chrysta Bell). She draws her pistol in "Part 16" (S3E16).
Revolvers
Smith & Wesson Model 19
Several deputies of the Twin Peaks Sheriff's Department are armed with the Smith & Wesson Model 19 in addition to Sheriff Frank Truman (Robert Forster). A similar revolver is seen in the hands of FBI Deputy Director Gordon Cole (played by film director and series creator David Lynch) in "Part 17" (S3E17).