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".
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.
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.
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.
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 waapon in the season 3 premiere.
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".
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.
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!".
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.
Season 3 Ep 4 Punked murder revolves around a death by a 200 year old dueling pistol. most notibly used by Detective Beckett, and Castle at a firing range to see how inaccurate they are. they humorously managing to hit everything down range but the targets, even shooting of the lain number above the target. Castle at one point duck-taps a laser and a scope on the gun, which doesn't help.
