Dean (Jensen Ackles) uses a customized Colt M1911A1. 45 pistol throughout the series as his weapon of choice. Dean's gun has engraved floral symbols along the slide, has mother of pearl grips and is chrome plated. John Winchester (Jeffrey Dean Morgan) is also seen using a M1911A1.
Taurus PT92
Sam Winchester (Jared Padalecki) uses a nickel Taurus PT92 with pearl grips as his weapon of choice. This weapon is also used by Dean Winchester (Jensen Ackles) several times throughout the series.
Colt Patterson 1836 aka The Colt
The legendary revolver that can kill anything. Built by Samuel Colt himself for a hunter (although it's thought that he built it for himself). The night that Halley's Comet flew over head and the night that all the men died at the Alamo, Samuel Colt created this weapon, along with 13 silver cartridges. He carved a pentagram into the handle, engraved a quote from the 23rd Psalm, and a high priest blessed it.
The Colt is passed to John Winchester by Daniel Elkins along with five remaining cartridges of the original 13 (Dead Man's Blood). Cartridge 9 was used by John Winchester on vampire Luthor to save Sam Winchester's life ("Dead Man's Blood"); cartridge 10 was used by Sam shooting at the Yellow-Eyed Demon in baby Rose's nursery, but he missed ("Salvation"); cartridge 11 was used by Dean to kill Demon Tom who was beating Sam senseless ("Devil's Trap); cartridge 12 was used by Sam to shoot John in the leg after he'd been possessed by Azazel (The Yellow-Eyed Demon). John then traded the Colt in a deal with Azazel to save a dying Dean...but the Winchester's later re-gained the gun and Dean used the remaining cartridge to kill Azazel.
Later in the series, Dean is shown going back in time to 1973 where he steals the Colt to shoot at the YED in that time period (but he misses)--so, technically, that means Dean uses up cartridge number 8 of the original 13.
Afterwards, Bobby and Demon Ruby figure out how to make the gun kill demons once again. The gun was also used as the key to a gate to Hell in Wyoming, which was surrounded by churches built by Samuel Colt in the 1800's (which is a major reason why I think he was a hunter). Although the gun can kill anything, it only has 5 shots, and has to be taken completely apart in order to reload the pistol.
In the fifth season episode "Abandon All Hope..." Dean uses the Colt to shoot Lucifer but it does not kill him. According to Lucifer there are five things in creation that the Colt cannot kill, him being one of them.
Beretta 92FS
Beretta 92FS pistols are frequently seen throughout the series. Sam and Dean are very rarely seen with them. Used by the Sheriff in "Dead In The Water".
Desert Eagle
Dean keeps a Desert Eagle in the trunk of his car and uses it once during Season 1. Bela uses a Desert Eagle to threaten the Winchester brothers in Season 3. Sam uses a black Desert Eagle in the season 6 episode "Unforgiven."
A possessed FBI agent tries to assassinate the Winchester brothers before being disarmed by Sam.
Jericho 941
Used by a former Marine named Sarge.
Glock 19
Used by a police detective played by Linda Blair.
Glock 17
Used by FBI agents, including Victor Henrickson. Dean is briefly seen holding one in Season 3 and in promotion photos. Security guards in "Phantom Traveler" are armed with Glocks.
Unknown Revolver
After escaping a police station, Dean steals an unknown revolver. Another is used by Ellen, who under demon control pointed it at her own head.
Single Action Army Artillery Revolver
Bobby Singer (Jim Beaver) carries a Single Action Army with 5.5" barrel and wood grips. It's lack of a 4th frame screw strongly hints that it is either a Cimarron or Uberti.
Walther PPK/S
Bela uses a stainless PPK/S
Heckler & Koch MK23
Used by Gordon whilst in a fire fight with Dean and Sam. Future Dean also uses one of these in the flash forward episode 'The End' carried in a thigh holster, which he uses to execute one of his resistance fighters who has been infected with the croatoan virus. Sam uses an MK23 as his standard sidearm starting in Season 6 Episode 2 "Two and a Half Men" and uses it until the episode "Unforgivien" where he switches back to his Taurus PT99.
Shotguns
Baikal Side-by-Side Sawed off IZH43 Shotgun
Dean (Jensen Ackles) frequently uses a Baikal sawed-off shotgun loaded with rock salt throughout the series.
Fairly certain that Dean's Baikal is a sawn-off Baikal IZH43. - Matt
Ithaca 37
Sam's carries a Ithica 37 as his standard shotgun loaded with rock salt throughout the series.
Remington 870
John gives Dean a Remington 870 shotgun in a flashback when he goes on a hunt.
Dean (Jensen Ackles) used this briefly in Season 2 Episode 5 "Simon Said." He was about to snipe a baddie, but was mind-controlled into trying to kill himself. Dean also uses this rifle in Season 6 Episode 8 "All Dogs Go to Heaven" to take out several skinwalkers.
Unknown Sniper rifles
Used by Police Snipers to gun down Ron during the "bank robbery".
By the looks of it the rifles are Remington M40s although as they're police, its more likely they are M24s or R700s, hard to tell due to the lighting though.
Remington 7600
A redneck used this rifle until Sam knocks him out, but he couldn't get it to work.
Unknown Rifles
There are seveal unknown rifles used throughout the series.
Heckler & Koch SL8
A Heckler & Koch SL8 is used by Victor. It has been upgraded with the SL8 sniper kit (threaded barrel, low profile scope rail). Also used by one of Deans resistance fighter's in the episode 'The End' fitted with what looks like a silencer and a scope.
M16 with A2 style handgrips
Used by conspiracy theorist Ron, who takes over a bank in hopes of killing a Shapeshifter, which he thought was a terminator. When Ron is gunned down by snipers, Dean takes the weapon and carries it through the rest of the episode.
I believe he thought it was a mandroid
MP5A3
Used by SWAT teams in several episodes. Also used by future Dean and future Castiel fitted with scopes and flashlights.
This is just his dads weapon stash from the truckzilla's trunk
-Close. The weapon loadout is slightly different, also Sam has changed the symbol at the top to a Crucifix, and removed the second Crucifix between the revolver and the pistol on the middle left side.