An AMT Backup pistol is used by Yvette Ellison as a murder weapon in "While You Were Sleeping".
Beretta 92FS
Holmes test fires a Beretta 92FS he found in Detective Bell's house in "Details". Harold Dresden (Richard Bekins) uses one after he disarms a NYPD plainclothes officer of his sidearm in "The Red Team".
Colt MK IV Series 80
Raul Ramirez uses a Colt MK IV Series 80 with a stainless slide in "You Do It to Yourself".
Glock 17
A Glock 17 is seen in the hands of a few NYPD ESU officers as one of their main sidearms in tactical operations. It's also seen in a computer screen at a NYPD detective's office table in "A Giant Gun, Filled with Drugs". An injured security guard fires his Glock 17 at Alysa and her robbery crew in "Snow Angels". Isaac Proctor (Erik Jensen), an assassin working for Moriaty, uses a Glock 17 after he goes rogue in "The Woman". Jordan Conroy (Dominic Fumusa), a security contractor from Lexicon Personal Security and agent of Moriaty, executes Christos Theophilus as the fall guy for an assassination against a prominent Macedonian national in "Heroine". Detective Marcus Bell (Jon Michael Hall) appears to be armed with a Glock 17 as his main sidearm.
Glock 19
A Glock 19 is used as one of the standard sidearms of uniformed NYPD officers. Serial killer Martin Ennis (Terry Kinney) takes a Glock 19 from a New York State Department of Corrections and Community Supervision guard after he's killed in "The Deductionist". Holmes shows off a Glock 19 to Ennis near the end of the same episode to see if he'll turn himself in or try to resist being captured alive. Detective Marcus Bell (Jon Michael Hall) appears to be armed with a Glock 19 as his main sidearm.
Heckler & Koch P7
What appears to be a Heckler & Koch P7 with a nickel-plated slide is used by a Dominican drug cartel gangster in "A Giant Gun, Filled with Drugs".
Mauser C96
A Mauser C96 is used by a home invasion suspect as a murder weapon in "One Way to Get Off". Holmes and Watson secure the C96 hidden underneath the wooden floorboards of a suspect's hotel room.
Sig Sauer P226
Corrupt Drug Enforcement Agency officer Xande Molina (Michael Irby) takes aim with a Sig Sauer P226 at Joan and Rhys in "A Giant Gun, Filled with Drugs".
Walther PPK
A Walther PPK was used by a dirty cop in "Details" as part of a plan to frame Detective Bell. During a debriefing, the pistol in question was chambered to fire .22 LR.
Non-Gun Version
A Non-Gun version of the PPK was used by Elle Bastien aka Alysa Darvin (Jill Flint) during a robbery in "Snow Angels".
A Smith & Wesson Model 65 was seen in the Pilot episode when NYPD officers found in the hands of Peter Saldua (Craig Walker) after his corpse was uncovered.
A Smith & Wesson Model 681 is used in the revolver wheel, changing from the Taurus Model 689 in the opening sequence.
Taurus Model 689
Taurus Model 689 revolvers are used in the opening sequence of Elementary in a revolver wheel.
Submachine Guns
Heckler & Koch MP5 (unknown model)
This unknown MP5 was used in "Details" during the attack on Detective Bell's sedan. The show does not exactly depict what type of MP5 is used. It isn' a MP5KA1 or MP5KA5, because they have different sights.
Assault Rifles
Colt Law Enforcement Carbine
Colt Law Enforcement Carbines are seen in the hands of the NYPD's Emergency Service Unit in tactical operations.
Shotguns
Benelli M4
A Benelli M4 was used in a door trap in a suspect's apartment room in "The Red Team", rigged to fire shotgun shells loaded with rock salt instead of buckshots when two NYPD officers entered the apartment, which unfortunately started the trap.
Others
Arsenal
NYPD officers uncover a small arms cache in "The Red Team".