An M14 Rifle is seen amongst the weapons wielded by the black ops soldiers in "731" (S3E10).
Remington 870 Shorty Custom
Customized Remington 870s are seen wielded by several FBI agents conducting an entry and arrest near the beginning of "Grotesque" (S3E14). The shotguns feature short barrels and forends with Butler Creek tactical synthetic loop pump-grips, forend mounted weaponslights, pistol grips with full buttstocks, as well as heatshields over the barrels and door-breaching muzzle brakes. Though some of these features are not clearly seen, they match those of custom Remington 870s that have appeared in the films Timecop, Crying Freeman, and several other movies and TV shows filmed in British Columbia. One of these shotguns also previously appeared in the first season, lacking the weaponlight and full stock.
Ithaca 37 "Stakeout" (Custom)
A custom Ithaca 37 "Stakeout" with a chrome finish on the barrel and magazine tube and an MP5K-style pump-grip is briefly glimpsed in the hands of FBI agents in "Grotesque" (S3E14) and "Pusher" (S3E17). This gun can also be seen in several episodes of the television series Supernatural, Human Target, Painkiller Jane, and several other TV shows filmed in British Columbia.
Franchi SPAS-12
What appears to be a Franchi SPAS-12 is very briefly seen in the hands of one of the black ops soldiers searching for Mulder in "Nisei" (S3E09).
USAS-12 CQ
What appears to be a USAS-12 Shotgun is seen wielded by one of the black ops soldiers guarding what appears to be a recovered UFO in "Nisei" (S3E09).
Trivia
In "War of the Coprophages" (S3E12), Scully is seen clearing her S&W 5906. A rarity in most films and TV shows, this is the first time in the series such an action is performed on-screen by one of the main actors.