Lieutenant Kitsurubami carries two Nambu Type 14 pistols as her sidearm.
Beretta 92FS
In episode 5, a billboard hit by a stay shot during Haruhana's battle with the giant robot depicts a man holding a Beretta 92FS pistol. This is one of several references to John Woo's films throughout the OVA.
M1911
Commander Amarao uses a pair of M1911 pistols as his primary weapons.
Glock 17
One of the Interstellar Immigration Bureau agents during episode 5 is armed with a Glock 17 pistol.
Unidentified Revolver
During episode 5, anytime Naota gets an idea, it's represented by an x-ray image of a revolver being cocked.
Submachine Guns
Beretta M12
One of Amarao's backup gunmen is armed with a Beretta M12 submachine gun.
One of the IIB agents is seen with an IMI Uzi with the same configuration as Haruhara's airsoft Uzi.
Rifles
Anti-Tank Rifle
In episode 5, Kitsurubami interrupts the airsoft game by firing at the players with an anti-material rifle of an unidentified make.
Steyr AUG A1
One of the IIB agents is armed with a Steyr AUG A1 assault rifle.
M16A1
One of the IIB agents is armed with a M16A1 assault rifle.
Other
Rickenbacker 4001
Haruhara's Rickenbacker 4001 bass guitar is seen being used as something other than a musical instrument on several occasions, including an automatic shotgun (with a rifled barrel) during the gunfight during episode 5.
Misc. Weapons
Several of the agents from the Interstellar Immigration Bureau use weapons that are never seen clearly enough to positively identify or are drawn in a generic style.
Airsoft Guns
A large portion of episode 5, Brittle Bullet, centers around an airsoft game between several of the series protagonists. Given FLCL's tendency towards exaggeration, these replicas are shown ejecting brass and having muzzle flashes with each shot.
MAC-11
Naota Nandaba uses a pair of MAC-11 submachine guns during the airsoft game.
Uzi
Haruko Haruhara's airsoft gun of choice is an Uzi with a wood stock and handguard.
Franchi SPAS-12
During the airsoft game, Kanti uses a Franchi SPAS-12 shotgun. In addition to being portrayed as if it were a live-fire weapon, it is seen being fired on full auto (while the real SPAS-12 can only fire either pump-action or semi-auto.)
Luger P08 "Artillery" Model
Kamon Nandaba's preferred airsoft weapon is a pair of Luger P08 "Artillery" Model pistols. He also has shoulder stocks attached to them in several scenes.
Over-sized Weapons
The giant robot in episode 5 is seen using several gargantuan firearms. As opposed to most mecha in anime that use specialized weaponry, this one uses weapons that are simply regular firearms that are scaled up to match its size.
On a side note, the battle between Haruhara and the robot (especially Harhara's bunny-girl outfit) is a self-referencing parody of the Daicon III and Daicon IV shortfilms that marked the animation debut of Studio Gainax's founders.
Winchester Model 1894
The first weapon that the robot uses is a scaled-up Winchester Model 1894 lever-action rifle with a sawed-off stock.
Colt Peacemaker
When Haruhara closes the distance between her and the robot, it responds by drawing an over-sized Colt Peacemaker revolver.
Mauser C96
When it realizes that it's losing, the robot produces a third weapon, a giant Mauser C96 pistol.
Miscellaneous Weapons
One shot shows Hruhara staring down five different weapons wielded by the giant, the three previously listed weapons as well as two gun barrels that do not appear in any other shot.