An AMT Backup pistol is used by Yvette Ellison (Amy Landon) as a murder weapon in "While You Were Sleeping" (S01E02).
Beretta 92FS
Harold Dresden (Richard Bekins) uses Beretta 92FS, taken from a disarmed NYPD detectivein "The Red Team" (S01E13). Sherlock Holmes (Jonny Lee Miller) test-fires one that he found in Detective Bell's apartment in "Details" (S01E16).
Colt MK IV Series 80
Raul Ramirez (Lord Jamar) uses a Colt MK IV Series 80 with a stainless slide in "You Do It To Yourself" (S01E09).
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" (S01E15). An injured security guard fires his Glock 17 at Alysa Darvin and her robbery crew in "Snow Angels" (S01E19). Isaac Proctor (Erik Jensen), an assassin working for Moriarty, uses a Glock 17 after he goes rogue in "The Woman" (S01E23). Jordan Conroy (Dominic Fumusa), a security contractor from Lexicon Personal Security and agent of Moriarty, executes Christos Theophilus as the fall guy for an assassination against a prominent Macedonian national in "Heroine" (S01E24). Detective Marcus Bell (Jon Michael Hill) 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 the same weapon to Ennis near the end of the same episode to see if he'll turn himself in or try to resist being captured alive.
Heckler & Koch P7M13
What appears to be a Heckler & Koch P7M13 with a nickel-plated slide is used by a Dominican drug cartel gangster in "A Giant Gun, Filled with Drugs" (S1E15).
Heckler & Koch USP Compact
Jamie Moriarty (Natalie Dormer) is seen with a compact pistol that resembles a Heckler & Koch USP Compact in "The Woman" (S1E23). Upon closer inspection, this pistol appears to be resin prop replica.
Mauser C96
A Mauser C96 is used by a home invasion suspect as a murder weapon in "One Way to Get Off" (Episode 1.07). Holmes and Watson secure the C96 hidden underneath the wooden floorboards of a suspect's hotel room.
SIG-Sauer P226
DEA Agent Xande Molina (Michael Irby) takes aim with a SIG-Sauer P226 at Joan and Rhys in "A Giant Gun, Filled with Drugs" (S1E15).
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" (Episode 1.19).
A Smith & Wesson Model 386 was used by Christos Theophilus (Arnold Vosloo) to execute a Macedonian surgeon and his wife in "Heroine".
Note: The cut in the grip, lack of marking, together with the safefy instructions under the cylinder release, suggests this is a WinGun CO2 airsoft revolver replica of the Smith & Wesson 386.
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" (Episode 1.16) during the attack on Detective Bell's sedan. The show does not depict exactly what type of MP5 is used, only that it has a rifled barrel and was fired in three-round bursts, instead of fully automatic.
A Benelli M4 was used to booby-trap the front door of Walter McClenahan's (Michael Laurence) apartment room in "The Red Team", triggered when two NYPD officers entered the apartment. Fortunately for them, the shells were loaded with rock salt instead of buckshot.
Others
Arsenal
NYPD officers uncover a small arms cache in Walter McClenahan's (Michael Laurence) apartment in "The Red Team".