Early in the first season, FBI Special Agent Fox Mulder (David Duchovny) carries a Taurus PT92 as his sidearm. He carries the weapon beginning in "Pilot" (S1E00) until last carrying it in "The Jersey Devil" (S1E04). Mulder fired the Taurus only once during this time, in "Conduit" (S1E03) to chase away a pack of wolves. A Taurus PT92 is also notably seen wielded by a member of the Arctic Ice Core expedition in "Ice" (S1E07), though later it becomes an actual Beretta 92FS. Taurus PT92s are also seen carried by police and government officers throughout the season (primarily in the earlier episodes), as well as soldiers and military personnel as a Beretta M9 stand-in.
Glock 19
After a few episodes in the first season, Mulder switched to a Glock 19. He carries it as his sidearm for the remainder of the season, (from "Shadows" (S1E05) to the season finale "The Erlenmeyer Flask" (S1E23)) with the exception of a single scene in the episode "Ghost in the Machine" (S1E06). A Glock 19 is carried by Claude Peterson (Blu Mankuma), an undercover government agent posing as a building engineer in that scene in "Ghost in the Machine" (Likely Duchovny's Glock, which would explain why he uses a different gun for only that particular sequence). Scully also briefly handles Mulder's Glock in "Ice" (S1E07). Glock 19s are also seen throughout the season wielded by police and government officers and military personnel, notably by several of the elite recovery soldiers in "Fallen Angel" (S1E09).
Bernadelli Model 60
Early in the first season, FBI Special Agent Dana Scully (Gillian Anderson) carries a Bernardelli Model 60 .32 ACP pocket pistol as her sidearm. She carries the weapon beginning in "Pilot" (S1E00) until "Ghost In The Machine" (S1E06). The pistol is a single action straight blowback weapon with a frame-mounted manual safety. The Model 60 was introduced in 1959, the magazine release is located at the butt of the pistol grip. It features a "VB" logo (Vincenzo Bernardelli) on the left grip. Scully's Model 60 has brown grips.
Manurhin PPK
After a few episodes in the season, Dana Scully (Gillian Anderson) switched to a Manurhin PPK .32 ACP as her sidearm. The Manurhin PPK is a French clone of the German Walther PPK made under the license of Walther. Scully carries the weapon starting in "Ice" (S1E07) and carries it for the remainder of the season. In "Fallen Angel" (S1E09) the Manurhin PPK had a misfeed, perhaps because Scully didn't rack the slide with enough fervor. Scully's PPK is also taken and briefly used by an FBI Agent (possessed by the reincarnated spirit of a career criminal) in "Lazerus" (S1E14).
Beretta 92FS
Throughout the season (Primarily in later episodes), actual Beretta 92FS pistols are seen used by police officers and government/military personnel, rather than Taurus PT92s. A Beretta 92FS is notably carried and used in "Lazerus" (S1E14) by Special Agent Jack Willis (Christopher Allport) and female career criminal Lula Phillips (Cec Verrell).
Smith & Wesson 5904
For a single scene in "Ghost in the Machine" (S1E06), instead of his regular Glock 19, Mulder carries what best appears to be a early-version blue-steel Smith & Wesson 5904, which he is seen unloading at gunpoint. The pistol features several characteristics of the early 5904s, notably the slightly curved backstrap and squared-off trigger guard.
Beretta 'Cheetah'
A Beretta Cheetah is used by Dr. Sally Kendrick/'Eve 6' in "Eve" (S1E10). Another Beretta Cheetah is used by an aeronautical scientist in "Roland" (S1E22).
M1911A1
A standard M1911A1 pistol is seen brandished in "Lazerus" (S1E14). What appears to be a stainless (or possibly nickel) M1911A1 is seen in the hands of an Atlantic City Police SWAT officer in "The Jersey Devil" (S1E04).
Desert Eagle
A polished stainless (or possibly chrome/nickel) Desert Eagle is seen as the sidearm of U.S. Air Force Colonel Calvin Henderson (Marshall Bell), the elite recovery unit commander in "Fallen Angel" (S1E09). It is only seen in his holster, and never used.
Unknown Pistol
An unknown stainless semiauto is seen carried by 'Deep Throat' (Jerry Hardin) at the end of "E.B.E." (S1E16).
Revolvers
Ruger Speed Six Snub
What appears best to be a Snub-Nosed Ruger Speed Six is seen twice in the season - First in "Ice" (S1E07) wielded by one of the Arctic Ice Core expedition crew members in a standoff with another crew member armed with a Taurus PT92, and then near the end of "Born Again" (S1E21) by a Buffalo police detective.
Single Action Army
What appears to be a Single Action Army or other SAA/'Peacemaker'-type revolver is carried by Indian Reservation Sheriff Charles Tskany (Michael Horse) in "Shapes" (S1E18)
Taurus Model 66
A full-size stainless revolver (Most likely a Taurus Model 66) is wielded by a genetically regenerated and altered convicted killer (previously taken down by Mulder) near the end of "Young at Heart" (S1E15).
Unknown Revolvers
Several unknown revolvers are seen in the show, wielded by police officers and/or FBI agents.
Shotguns
Mossberg 500 (Numerous Variants)
Several types of Mossberg 500 shotguns are seen throughout the season - Due to the number of different variants, they will be sub-divided within this section. Note that it is possible some of these might actually be the lower-priced Maverick 88 models, as the show rarely gives good showings of the weapons' receievers (the safety placement being the only readily distinguishable difference between the two) and at least one Maverick 88 is actually seen used in the show as well.
Mossberg 500 'Persuader'
Several standard riot-model Mossberg 500s, known as 'Persuader' models, are seen throughout the season, and indeed are the most common variant seen. They are used by numerous police and government agents, as well as seen in the hands of some military personnel.
Mossberg 500AT
Some of the Mossberg shotguns appear to be Mossberg 500AT variants, noted by the wooden foregrip.
Mossberg 500 Bullpup
A Mossberg 500 Bullpup is seen used by at least one of the elite recovery soldiers in "Fallen Angel" (S1E09).
Mossberg 500 'Cruiser'
Pistol-gripped Mossberg 500 Cruisers are seen used by some police and government agents, notably by agents conducting a raid near the end of "Lazerus" (S1E14).
Mossberg 500 Field
A 'field' variant of the Mossberg 500, with long, ribbed barrel and wooden furniture is seen carried as a main weapon by Steve Humphreys (Tom O'Rourke), a lumber company security chief, in "Darkness Falls" (S1E19).
Maverick 88
During the opening sequence in "E.B.E." (S1E16), a truck driver is seen brandishing a Mossberg-manufactured Maverick Model 88 shotgun. The gun appears to be set-up in a kind-of 'Cruiser' configuration - It appears to have a pistol grip and riot-length barrel, however the barrel is ribbed, and the weapon features a top-folding stock. It is noted as a Maverick and not a Mossberg 500 due to clear showing of the button-safety located on the front tang of the trigger guard (Actual Mossbergs feature a switch safety at the top-rear of the receiver).
Remington 870
A standard Remington 870 is seen carried by a New Jersey state trooper in "The Jersey Devil" (S1E04).
Remington 870 Shorty Custom
A customized Remington 870 is seen wielded by career criminal Warren James Dupre (Jason Schombing) to commit a robbery and attempt to kill an FBI agent at the beginning of "Lazerus" (S1E14). The shotgun features a short barrel and forend featuring a Butler Creek tactical synthetic loop pump-grip, along with a pistol grip and heatshield over the barrel. This is the exact same custom Remington 870 that appeared in Timecop, Crying Freeman, and quite a few other movies and TV shows filmed in British Columbia, though in this episode, the weapon has been fitted with a pistol grip rather than the combination pistol grip/stock seen in subsequent appearances (undoubtedly, the latter feature was added by the armorers later on).
Side-by-Side Double Barrel Shotgun
Several Side-By-Side Double Barrel Shotguns are seen used by police officers and deputized citizens conducting a search party at the beginning of "The Jersey Devil" (S1E04).
Over/Under Double Barrel Shotgun
An Over & Under 12-Gauge Double Barrel Shotgun is used by a ranch owner to kill a supposed 'wolf monster' (that turns into a regular man) at the beginning at "Shapes" (S1E18).
Assault Rifles / Carbines
Colt Commando
Numerous episodes in Season 1 feature appearances of Colt "Commando"-type carbines, usually in the hands of military personnel and SWAT officers. There's a great close-up of one of these weapons in "Deep Throat" (S1E01). The weapons feature A1E1 receivers (noted by the A1-sights, brass deflector and full magazine fence), however these are not Model 733s, as these weapons feature what seem to be very short (Roughly 10") barrels, shorter than the M733's 11.5" barrel. Most likely, these are Olympic Arms K3B carbines that had their barrels cut down, given that the A1E1 receiver style was common on Olympic Arms rifles made in the 1990s.
Colt AR-15 SP1 (Mocked Up as M16A2)
In several episodes, U.S. military personnel are armed with Colt AR-15 SP1 rifles with M16A2-style hand guards, standing in for the M16A2 service rifles that the soldiers should be using in real life. You can tell because the receivers of the guns don't have the "fencing" around the magazine release, plus they lack the A2-style rear sights, shell deflectors, and forward assists. These are not fired on the episode, but they can be full auto conversions since armorers in both Canada and the U.S. picked up many SP1 conversions during the 1970s and 1980s.
Diemaco C7-Etc
Due to the series' filming in Vancouver, British Columbia, Canada, most of M16-type rifles seen throughout the season were Diemaco C7s, or, more likely, the Olympic Arms K4B equivalent, which seems to be favored by the Canadian armorers. These weapons appeared in the hands of U.S. military personnel as an M16A2 stand-in, particularly in the episodes "Deep Throat" (S1E01) and "Fallen Angel" (S1E09).
Muzzelite MZ14 Bullpup
A Muzzelite MZ14 Bullpup (The bullpup configuration for the Ruger Mini-14) is seen wielded by at least one of the elite recovery soldiers in "Fallen Angel" (S1E09), probably chosen for it's 'futuristic' appearance.
Rifles
M1 Garand
Standard M1 Garand rifles are seen in two instances in the show's first season. One is wielded by a deputized citizen as part of a search party in "The Jersey Devil" (S1E04). Another is seen wielded by a honor guard member at the end of "Space" (S1E08).
Tranquilzer Rifle
A Traquilizer Rifle is used by a New Jersey Forest Service Ranger in "The Jersey Devil" (S1E04).
Remington 700 BDL
What appears to be a Remington 700 BDL bolt-action rifle is used by a rancher's son at the beginning of "Shapes" (S1E18).
Winchester Model 1894
What appears to be a Winchester Model 1894 lever-action rifle (or clone/copy) is seen carried by a Native American wise man, Ish (Jimmy Herman) in "Shapes" (S1E18).
Unknown Bolt-Action Rifles
Numerous other bolt-action rifles are seen through the series' first season, some appear to be more regular hunting rifles (as seen used by officers and deputized citizens in "The Jersey Devil" (S1E04)), and some are tactical sniper rifles (as seen used by FBI tactical agents in "Lazerus" (S1E14)).
Unknown Rifle
An unknown sporting/hunting-style rifle is seen wielded by a trucker in "Eve" (S1E10). The rifle does not appear to have a bolt-action (either straight or pull). It also has a considerably large rounded chamber and receiver. It may be some type of revolving rifle, or simply perhaps an air rifle or other prop.
Submachine Guns
Heckler & Koch MP5A3
Several Heckler & Koch MP5A3s are seen throughout the season, close inspection shows the vast majority in Season 1 are actually Tokyo Marui spring-powered airsoft guns. They are wielded by police tactical officers and government agents, as well as military personnel, notably by several of the elite recovery soldiers in "Fallen Angel" (S1E09).
(Mock-up) Heckler & Koch MP5K
Some Heckler & Koch MP5Ks are seen used by government and military personnel. Notice that these are not real MP5Ks; they are actually mock-ups built on the bolt carrier and magazine well of a Kimel AP-9, because the armorers in British Columbia did not have genuine MP5Ks during the 1990s. The same guns have also appeared in Crying Freeman, M.A.N.T.I.S., and The Outer Limits.
Unknown SMG
Several unknown submachine guns are seen used by the elite recovery soldiers in "Fallen Angel" (S1E09). This SMG has appeared in many movies and TV shows filmed in British Columbia, including The X-Files, M.A.N.T.I.S., Timecop, Rumble in the Bronx, Viper, and Smallville (among others), but IMFDB has yet to identify these weapons.
Other
M60 Machine Gun
Standard M60 machine guns are seen used by military personnel, primarily mounted on military Jeeps and HMMWVs, one is notably seen mounted on a M151 MUTT in "Fallen Angel" (S1E09).
Guns in Police Photograph
In "Born Again" (S1E21), a police photograph is viewed, showing what is apparently the confiscated proceeds of a major bust, including a large number of mixed firearms.