A Glock 26 is carried by Beckett as her backup. This pistol is seen used by Castle in order to defend himself in the Season 3 premiere "A Deadly Affair" (S3E01).
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 catalyst sitting on his bookshelf. A catalyst is required for any Firefly class ship to run, and was a large part of Out of Gas' story arc.
In "The Third Man" (S2E14), Noel du Preez (Michael Enright) uses a compensated M1911-type 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 in "Den of Thieves" (S2E21), off camera Esposito uses it to wound dirty Lt. Holliwell. A 1911 is found to be the murder weapon in Season 3's premiere "A Deadly Affair" (S3E01).
The killer uses a Ruger P90 during his activities in "Boom!" (S2E18). FBI Special Agent Jordan Shaw (Dana Delany) briefly uses it near the end of the same episode.
NYPD officers are occasionally carrying the SIG-Sauer P226 (in reality, this weapon is not authorized by the NYPD to carry onduty). After disarming an officer, Rathborne holds Castle hostage with one in "Sucker Punch" (S2E13).
In "Under the Gun" (S3E03), Gayle Carver (Sophina Brown) is seen wielding this gun during a confrontation between the detectives Mike Royce (Jason Beghe) and Clifford Stuckey (James Handy).
Montgomery uses a Bond Arms Snake Slayer IV Derringer as his holdout weapon during his confrontation with Lockwood in Season 3's finale "Knockout" (S3E24). It is the IV version of the Snake Slayer as noted by its longer barrel, and although normally chambered in .45 this pistol appears to use the .38/.357 barrel, as Montgomery loads it with the same rimmed rounds he uses in his revolver.
In "Punked" (S3E04), 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.
A Smith & Wesson Model 19 is seen loaded by Captain Roy Montgomery (Ruben Santiago-Hudson) in Season 3's finale "Knockout" (S3E24). He later seen with in the hangar in the episode.
Bail bondsmen Deon Carver is seen brandishing his Model 60 when he returns to his office and notices somebody has broken in. Castle is seen holding a snubnose revolver as Beckett, Ryan & Esposito clear a murder victim's apartment.
Castle (Nathan Fillion) is briefly seen dressed in a costume deliberately similar to that worn by Captain Malcolm "Mal" Reynolds in the series Firefly (Fillion's former television series). Castle is even seen wielding the modified Taurus 85 when trying his Mal costume on during the opening sequence of "Vampire Weekend" (S2E06). In Firefly, the revolver was known as a "Moses Brothers Self-Defense Engine Frontier Model B".
While searching Kyle Cabot's apartment, Esposito finds what appears to be a Jennings J-22 compact pistol in the series premiere "Flowers for Your Grave" (S1E01).
In "Punked" (S3E04), Castle is seen wielding what appears to be a custom engraved replica of a Colt 1851 Navy revolver while bursting through his front door and catching his daughter snogging her boyfriend.
An Heckler & Koch MP5A4 with a weaponlight, and Navy trigger group was used by a drug dealer while stealing a victim's body in Season 2's premiere "Deep in Death" (S2E01).
During the events of "A Deadly Game" (S2E24), an MP5K is found in the car of Roger Farraday (Dean Cates). 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 foreign 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 "Tick, Tick, Tick..." (S2E17) and "Boom!" (S2E18).
In "Vampire Weekend" (S2E06), Esposito (Jon Huertas) is seen carrying an MGC M16 replica fitted with an M203 grenade launcher during Castle's Halloween party while dressed up as a US Marine (an in-joke as Huertas portrayed US Marine Sgt. Antonio Espera in the HBO miniseries Generation Kill).
Esposito (Jon Huertas) uses a Remington 870 on multiple occasions throughout the season. In "Sucker Punch" (S3E13), the victim Jack Coonan (Justin Alvarez) had one loaded with hollow point slugs in his apartment.
In "Under the Gun" (S3E03), Mike Royce (Jason Beghe) is seen wielding what appears to be a Mossberg 500AT shotgun during a confrontation between the detectives, Gayle Carver (Sophina Brown) and Clifford Stuckey (James Handy).
In "Knockdown" (S3E13), Hal Lockwood (Max Martini) uses a suppressed ROCK SOPMOD M14 to shoot at John Raglan, and later during a shootout with Beckett. It appears to have a Harris bipod and AN/PEQ-2/5. It is supposedly chambered in .338, despite the round being much too large for fit the 7.62x51mm chamber.
A Knight's Armament SR-25 can be seen in Season 4's premiere "Rise" (S4E01). It is recovered after the attempted assassination attempt on Beckett, as seen in Season 3's finale "Knockout" (S3E24). Esposito refers to it as a Mk 11, which is correct as this particular rifle was a Navy SEAL issue weapon.
A Remington Model 700 AICS fitted with a suppressor and a Harris bipod is seen in "Kill Shot" (S4E09). The rifle is loaded with 165 grain .308 Winchester ammo.
In "The Final Nail" (S3E15), detectives arrive at the crime scene to find a female victim with multiple flat-head nails protruding from her skull. Behind a nearby chair they find a nail gun. It appears to be a cosmetically altered KitPro series judging by the shape of the butt, housing assembly (screws pointing aft), housing vents on the side and top, and the 'over/under' 'muzzle'. I think the 'over' is a nail depth gauge.
