The Glock 17 is the sidearm carried by both Detective Carlton Lassiter (Timothy Omundson) and Det. Juliet O'Hara (Maggie Lawson) in the first four seasons. Det. Lassiter is seen wearing his Glock in various shoulder rigs, even having a quick draw dual from his shoulder holster.
Colt 1860 Army
In "Weekend Warriors" (S1E06), Griffin Mahoney (Peter Michael Goetz) is seen showing off a collection of Civil War memorabilia, which includes several revolvers, including a Colt 1860 Army.
Smith & Wesson Model 15
In "Scary Sherry: Bianca's Toast", Detective Goochberg (Mercedes Ruehl) fires a Smith & Wesson Model 15 when taking target practice on the range with Det. Lassiter.
Smith and Wesson Model 629
In "Scary Sherry: Bianca's Toast", a Smith & Wesson Model 629 with rosewood grips and nickel finish is used by Detective Lassiter at the firing range and then used by his temporary partner Detective Goochberg (Mercedes Ruehl) who did not brace for the recoil and it (unrealistically) flies out of her hands and smashes into the wall breaking into several parts.
Walther P99
In the pilot episode, Lucinda (Anne Dudek) uses a Walther P99 at the police shooting range before handing the weapon off to Shawn Spencer (James Roday) who proceeds to fire several shots, each hitting adjacent to the Detective's hits.
In "Forget Me Not", Ranger DeSoto (Gardiner Millar) holds a Remington 870 on Shawn and Gus.
Rifles
M16A2
In the pilot episode, several SWAT officers are armed with the M16A2 during the raid on the house. Several SBPD Officers are seen holding the M16A2 when the police station goes into lockdown in Season 3's "Lassie Did a Bad, Bad Thing". There is two gun racks full of these in the military armory in Season 4's "You Can't Handle This Episode".
Springfield 1861
The Springfield 1861 rifle is used by Civil War re-enactors throughout "Weekend Warriors" (S1E06). The rifle also apparently was used to murder Nelson Poe (Yves Cameron). It's also seen being handled by Juliet later in the episode.