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".
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 Hill) appears to be armed with a Glock 17 as his main sidearm.
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.
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.
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".
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.
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.
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.
Colt Law Enforcement Carbines are seen in the hands of the NYPD's Emergency Service Unit in tactical operations.
Error creating thumbnail: File missingColt Law Enforcement Carbine - 5.56x45mm.Error creating thumbnail: File missingA Colt LE Carbine with picatinny railings and a mounted scope and tac light through a helmet cam in "Child Predator". It appears that the vertical foregrip wasn't used.Error creating thumbnail: File missingAnother LE Carbine seen in the middle of the helmet cam screens in the same episode. This time, it has a mounted red dot sight.Error creating thumbnail: File missingA NYPD ESU operator with a Colt LE Carbine without the carry handle attached in "The Deductionist".Error creating thumbnail: File missingA Colt LE Carbine used by ESU officers during a raid to search for Holmes and M in "M". Note the ACOG scope, the picatinny railing on the foregrip and the tac light attached on it.Error creating thumbnail: File missingAn ESU team prepares to breach a room near the conclusion of "The Red Team". Note that their LE Carbines are outfitted with ACOG scopes and vertical foregrips, except for the ESU operator at the left side of the photo. The ESU operator with a ballistic shield is armed with what seems to be a Glock 17.
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.