NYPD Detective's Javier Esposito (Jon Huertas) and Kevin Ryan (Seamus Dever) use a Glock 17 as their primary sidearms throughout the series. Detective Kate Beckett (Stana Katic) uses one until "Home is Where the Heart Stops". Criminals also like them, one was used with a suppressor to murder Roger Farraday (Dean Cates) in A Deadly Game.
Glock 19
Detective Kate Beckett (Stana Katic) starts carrying the more compact Glock 19 during the events of "Home is Where the Heart Stops". Castle (Nathan Fillion) also uses Kate's while at the range, pretending to be completely inexperienced, then showing extreme proficiency after he's offered crime scene photos. Det. Tom Demming (Michael Trucco) also carries one.
Glock 26
A Glock 26 serves as Det. Beckett's backup gun, it's most notably seen when she hands it to Castle to defend himself from the "Tick, Tick, Tick..." & "Boom!" killer when they enter the warehouse he's hiding in. He uses it to shoot Kate's Glock 19 out of the killers hand. After wards Castle reveals that "he was aiming for his head". Castle again uses Kate's Glock 26 in order to defend himself in the season 3 premiere A Deadly Affair, he uses it to wound a gunman who came up behind Beckett.
Noteworthy is that his "Aiming for the head" remark is the third Firefly/Serenity reference in the series. The first two took place during the episode "Vampire Weekend" when Castle wore his Mal costume, and the second was a catalyzer sitting on his bookshelf. A catalyzer is required for any Firefly class ship to run, and was a large part of Out of Gas' story arc.
1911
Noel du Preez (Michael Enright) uses a compensated 1911 to shoot at the team when he thinks they're robbers stealing from his store. Former NYPD officer, and Esposito's former partner Ike Thornton (Aaron D. Spears) is seen with a 1911 during Den of Thieves, off camera Esposito uses it to wound dirty IA Lt. Holliwell. A 1911 is found to be the murder weapon in the season 3 premiere. A murder suspect named Roland D'Andre (Randal Reeder) is found to have a Safari Arms Matchmaster 5 on him.
A two tone USP was used by the "Deep in Death" killer to threaten Castle, then by Beckett after she disarms him.
Jericho 941
Earl (Craig Gellis) is seen using a stainless Jericho to fire on Castle and company.
Ruger P90
The "Tick, Tick, Tick..." & "Boom!" killer uses this during his activities in "Boom!", FBI Special Agent Jordan Shaw (Dana Delany) briefly uses it near the end of the same episode.
SIG-Sauer P226
NYPD officers are occasionally seen with this weapon. After disarming an officer, Rathborne holds Castle hostage with one.
SIG-Sauer P232
Gayle Carver (Sophina Brown) is seen wielding this gun during a confrontation between the detectives, Mike Royce (Jason Beghe) and Clifford Stuckey (James Handy).
SIG Pro SP 2009
Jack Coonan (Justin Alvarez) had a 9mm SIG Pro in his waistband when he was killed in Sucker Punch.
Smith & Wesson Model 15
A Smith & Wesson Model 15 is used by the killer in "One Man's Treasure".
Smith & Wesson Model 60
Bail bondsmen Deon Carver is seen brandishing his Model 60 when he returns to his office and notices somebody has broken in.
Smith & Wesson Model 625
The weapon used to kill Max Heller (Creagen Dow) in "Hedge Fund Homeboys".
Smith & Wesson 3913
Owned by Jeremy Preswick (Marc Blucas), and used by Darius Langley (John Paul Pitoc) to kill Victor Fink and shoot Preswick.
Star Firestar M-43
Harrison Tisdale (Brian Avers) uses a stainless one in the pilot episode "Flowers for Your Grave".
STI 2011 Edge
An STI Edge is seen being handled by Ben Conrad, then used by Scott Dunn (Dameon Clarke) to execute him off camera.
Scarlett Price (Michaela McManus) used this pistol in "Love Me Dead".
Walther PPK
IA Lt. Stan Holliwell (Scott Cohen) uses a suppressed PPK near the end of the episode "Den of Thieves".
Undetermined Pistols
Semi-automatic .22 Pistol
While searching Kyle Cabot's apartment in the pilot, Esposito finds this compact pistol. This looks more like a Raven .25, and them calling it a .22 is just to fit the plot. You can see the Raven's mag release on the butt.
Stainless Snubnose Revolver
Castle is seen holding a snubnose revolver as Beckett, Ryan & Esposito clear a murder victims apartment.
Antique Revolvers
Castle is seen wielding one while bursting through his front door and catching his daughter snogging her boyfriend. Irwin Finkelstein is seen holding two antique revolvers in pictures on a antique firearms social networking page.
Flintlock Pistols
In Punked, Daniel Goldstein and Adam Murphy are found to have each used flintlock pistols in a duel to impress a woman. Later, while trying to determine whether to charge Adam with murder or manslaughter, they hilariously succeed at hitting everything in the range but the targets. After several failed attempts, Castle uses duct tape to attach a scope, and laser sight in a last ditch attempt to hit the target. Other models are also seen being held by Ivan Podofski (Muse Watson) in photos on a antique firearms social networking page.
Submachine Guns
Heckler & Koch MP5A2
An MP5A2 with a weapon light, and Navy trigger group was used by a drug dealer while stealing a victims body in the season 2 premiere, "Deep in Death".
Heckler & Koch MP5K-PDW
During the events of "A Deadly Game", an MP5K-PDW is found in Roger Farraday's (Dean Cates) car. It was issued to him as part of a "spycation" where Farraday, under the guise of CIA hitman Sean Caldwell, was supposed to "assassinate" a foriegn minister with it.
Assault Rifles
Heckler & Koch HK416
While not clearly seen, several FBI HRT agents use HK416's with 10" barrels.
M4A1
Esposito (Jon Huertas), as well as most NYPD ESU officers use M4A1's when needed. FBI HRT agents can be seen wielding both M4A1's and HK416's during the episodes "Tick, Tick, Tick..." & "Boom!".
M16A2
Esposito (Jon Huertas) is seen with one during Castle's Halloween party, dressed up as his Generation Kill alter-ego Sgt. Antonio Espera.
Shotguns
Remington 870
Esposito (Jon Huertas) uses a Remington 870 on multiple occasions throughout the season. In Sucker Punch, the victim Jack Coonan (Justin Alvarez) had one loaded with hollow point slugs in his apartment.
Unknown Shotgun
Mike Royce (Jason Beghe) is seen wielding this shotgun during a confrontation between the detectives, Gayle Carver (Sophina Brown) and Clifford Stuckey (James Handy).
Winchester 1300
Clifford Stuckey (James Handy) is seen using this shotgun during a confrontation between the detectives, Gayle Carver (Sophina Brown) and Mike Royce (Jason Beghe).