Nikita carries an .380 Auto AMT Backup as her backup weapon,carried in an ankle holster. She is seen with it in "The Guardian" (S1E5) after losing her P239 and in "One Way" (S1E9) when Michael forces her to drop all of her weapons.
Beretta 92FS
In the pilot episode, General Safwani's bodyguards all carry 92FS pistols. Roan (Rob Stewart), a Division cleaner carries two with him. Thom (Ashton Holmes) uses it as his main sidearm as a Division agent. Alex (Lyndsy Fonseca) and other Division agents use suppressed 92FS' under the disguise of pro-Georgian republicans in Coup De Grace. Alex uses a Beretta 92FS pistol taken from a bodyguard during the chem-lab shootout. After switching from his P226, Michael starts using a 92FS as his sidearm.
Beretta 92F - Non Gun
A Division agent forces Jill Morelli (Julie Gonzalo) to kill her boss with a non-gun Beretta 92.
Beretta 92FS Inox
Alex disarms a guard in the Zoman family estate in All the Way. This one is a Bruni blank firing gun, the finish isn't the same as a real stainless 92FS. Jaden (Tiffany Hines) uses a Beretta 92FS Inox that she took from a guard during the chem-lab shootout in Girl's Best Friend. Michael takes one from Percy in Pandora.
Beretta Px4 Storm
Alex is seen with a PX4 during "Betrayals"(S1E21) and "Pandora"(S1E22).
Glock 17
Michael (Shane West) is seen with a Glock 17 when confronting Nikita in her memory, interestingly he never uses a Glock in reality. Police officers use Glock 17s in "Phoenix"(S1E8). Ex-Guardian Dana Winters, in a shocking display of skill, uses one in "Glass Houses"(S1E20) to execute an entire Division strike team in seconds, headshots only. CIA security officers and Ryan Fletcher carry them in "Pandora" (S1E22)
A Glock 17 mounted on a CAA Tactical RONI-G1 can be barely seen with a shoulder sling on a Division operative after he and his team assassinate a chief editor to frame Jill. Sara (Alexandra Krosney) uses a RONI-G1 when she and Nikita fight off Division operatives, it appears to be fully automatic at this point and may be a modified Glock 17 or Glock 18. It is also the main weapon of Division operatives as a submachine gun/carbine-type weapon.
Glock 26
Nikita has a Glock 26 in her gun case. Emil Voss (Matthew Marsden) pulls a suppressed Glock 26 on Nikita in The Next Seduction, it's later handled by Nikita. During her hallucinations in Echo, Alex sees a future version of herself take one from a desk drawer.
SIG-Sauer P220
Though in every other scene he's using a SIG-Sauer P226, after Nikita (Maggie Q) takes Michael's (Shane West) weapon it becomes a SIG-Sauer P220.
SIG-Sauer P226
Aside from the end scene of the pilot, Michael's sidearm for the early portion of the first season is a SIG-Sauer P226. Robby uses his sidearm to kill a Division guard leader before he uses it to take Alex hostage in "The Recruit" (S1E7). CIA analyst Ryan Fletcher (Noah Bean) is armed with this in Chile before he is forced to drop it in "Dark Matter" (S1E10). Owen takes the P226 from Cleary (Michael Cram), a CIA agent stationed in Chile, on a MC-130 Hercules en route to the US. Division security personnel, most notably Robbie (Bug Hall) carry P226's as well.
SIG-Sauer P228
Division agents appear to be using P228's at the party in the pilot episode. Nikita disarms one of them and fires it. She also uses one when she tries to "rescue" the Senator from Division custody.
SIG-Sauer P239
Seemingly Nikita's preferred weapon throughout most of the first season is a SIG-Sauer P239. It is a stainless DAK model, and appears to have a Hogue wraparound grip. After taking it from Nikita, Owen uses one during Guardian. In The Recruit, Division recruit Sara (Alexandra Krosney) manages to get Nikita's P239 and hold her at gunpoint.
Walther P22
Alex uses a Walther P22 with a black slide in the chem-lab shootout in Girl's Best Friend, later passing it to Jaden. Jaden pulls her own Walther P22 on Alex later in Glass Houses and is shot with it in the ensuing fight. Percy offers Michael one to execute Alex in Betrayals, unfortunately it was modified to electrocute the shooter.
Walther P99
Nikita uses one to engage a Division guardian in Britain alongside Owen. Later in Glass Houses, Nikita is seen using a two tone model while searching guardian Dana Winter's former home.
Walther PPK - Non-gun
After an attempt on his life by Nikita and Michael in One Way, terrorist Kasim Tariq executes a colleague he believed betrayed him with a flashpaper Walther PPK.
Zoraki M906
A Zoraki M906 is used by Alex to execute her captors after being freed from captivity.
Zoraki 914
On several occasions, Zoraki 914 blank firing pistols are used. These pistols are capable of semi automatic and full automatic fire, and are used to substitute for conventional pistols and machine pistols.
Zoraki 925
Nikita acquires a Zoraki 925 blank firing pistol fitted with an extended magazine from a guard in Alexandra. Some of the guards uses what appears to be this weapon in Girl's Best Friend.
Revolvers
Chiappa Rhino 50DS
In "Covenants" (S1E17), Nikita seen using a Chiappa Rhino 50DS (5" barreled version) revolver during the shootout with Karim's men.
Smith & Wesson Model 629 Classic
Russian slaver Vladimir Ivanov (Mark Ivanir) is seen with an Smith & Wesson Model 629 Classic with a Classic Hunter barrel and front sight.
Submachine Guns
Heckler & Koch MP5A3
Among other Division recruits, Alex, Jaden (Tiffany Hines), & Thom (Ashton Holmes) are seen assembling MP5A3's as part of their training. Rospeta mercenaries working under Hanna are armed with the MP5A3, some of them suppressed when they battled Michael and his team in the New York subways. A Division operative handles on in the arsenal prior to securing Jill. In Coup de Grace Division agents are also seen using them in both the pre-operation exercise, and the actual operation to assassinate Prince Eric of Georgia.
Heckler & Koch MP5SD
Several MP5SD submachine guns are seen in a gun case in the background.
Heckler & Koch MP5K
Several MP5K submachine guns are seen in a gun case in Division HQ. Two Division agents assisting the London Guardian used MP5K's, Owen partially commandeered ones MP5K to kill the other.
IMI Uzi
Nikita has a full size Uzi in her gun cache. Kasim Tariq's (Haaz Sleiman) bodyguards ironically (See: Lord of War) use them in Uzbekistan.
FN P90
Division operatives use the standard P90 in All the Way, going in to help Alex by assassinating Gaddiel Zoman in his estate. Used by Nikita and Owen when they go into Chile and rescue a CIA analyst from leftist guerrillas.
Several P90TRs are seen in the gun case as well fitted with EOTech 552 sights. Several P90TRs with the sights removed were used by a team of recruits in a CQB training simulation, most notably Alex, Sara (Alexandra Krosney), and Robbie (Bug Hall). A Division guard is armed with a P90TR before Nikita disarms him in All the Way. They also appear as the standard issue weapon for GOGOL operatives.
Heckler & Koch MP7
Nikita retrieves two MP7 submachine guns from her weapons cache when her safehouse is stormed by Division agents in the Season 1 finale Pandora. She dual-wields them briefly before passing one of the guns to Alex.
Sa. Vz.61 Skorpion
One of the "kidnappers" in "Resistance" (S1E6) uses a Sa. Vz.61 Skorpion during the bus attack. Another is used by a GOGOL operative with a suppressor attached in Quebec.
Sterling Submachine Gun
One of the compound guards in "Girl's Best Friend"(S1E19) is armed with a Sterling after engaging Alex and Jaden (Tiffany Hines). It's not clear on the specific type.
Rifles
SIG SG 552
Division agents are seen with SIG SG 552s fitted with suppressors and C-More red dot sights in the pilot episode. The SIG SG 552 appears to be the stand-issue Division assault rifle and are used by Division personnel with, and without the suppressor and C-MORE sight. Percy uses one when he pursues Nikita and a wounded Owen in the port of Montreal. The Division agents assaulting Nikita's safehouse in "Pandora" (S1E22) are seen using them as well.
FN FS2000 Tactical
Michael, under the guise of a FBI HRT operator, is seen carrying a FS2000 rather than the M4A1's the rest of his team is using in "Coup de Grace" (s1E13). He does still use a C-MORE Tactical red dot sight like the rest of his team.
Heckler & Koch G36C
A Heckler & Koch G36C is seen in Nikita's weapon cache. Owen borrows it when he retrieves the black box in Montreal.
IMI Tavor TAR-21
As well as the SIG SG 552, Division agents also use Tavor TAR-21s, fitted with suppressors and Meprolight Mepro 21 sights in the pilot. It's later seen on Trevor's table, fitted with the same accessories.
M16A2
M16A2 rifles are used by US Army personnel in "Dark Matter" (S01E10).
M4A1
An M4A1 with a bipod, scope, laser aiming module with light and a suppressor is seen on a table displayed by Nikita's arm dealer contact, Trevor. Michael will later use this same rifle in "Rough Trade" (S1E4), "Dark Matter" (S1E10), and "Covenant" (S1E17). Other M4A1s fitted with M203 grenade launchers, are seen in the Division armory. A Division team led by Michael are using M4A1s while posing as FBI HRT (Hostage Resque Team) operators in "Coup de Grace" (S1E13).
FAMAS G2
FAMAS G2 rifles are seen in the Division armory, and the London guardians storage container but have yet to be fired in the series.
Zastava M70
Bank robbers in the opening to The Guardian use Zastava M70's, and Owen (Devon Sawa) seizes one to disrupt the robbery. Leftist guerrillas are armed with M70AB2s while in Chile. A Division operative disguised as a kidnapper uses M70s. Al-Qaeda terrorists near the Russian-Chechnya border armed with the M70.
Shotguns
Remington Model 870 Shotgun
One of the men at the CIA substation in Chile is seen drawing a shortened Remington Model 870 Shotgun when Ryan arrives. It is later seen carried by a leftist guerrilla after they storm the station. Michael is seen with a custom version with M4 stock and railed pump handle with folding foregrip in S1E16 "Echoes". Nikita caries a sawed-off model when she "robs" the bank in episode 20. A Division operative assisting Michael in an assassination op has the Police Version with a solid stock.
Serbu Super Shorty Remington 870 Shotgun
What appears to be a Serbu Super Shorty with a foregrip is carried by a robber in the "The Guardian" (S1E5).
Mossberg 590
Nikita uses a Mossberg 590 when rescuing Jill from Division in S1E3 "Kill Jill"
Unknown Shotguns
Two unknown shotguns are used by Alex and her accomplice (who was actually Nikita) in the drug store robbery in episode 1. I'm 97% sure Alex's is a Winchester 1300, but I'm not sure. And her accomplices is completely beyond me. A Division agent disguised as an HRT operator is seen with an unknown shot gun is "Coup de Grace" (S1E13
Sniper Rifles
Steyr HS.50
Nikita is seen using a Steyr HS.50 in the episode 2.0, acquired from an arms dealer named Trevor before she had a confrontation with him over killing her to get a reward from Percy. She uses it to shoot a Rospeta-linked mercenary attacking Michael.
Remington 700PSS
Michael uses a Remington 700 PSS sniper rifle fitted with a Schmidt & Bender scope when hunting down Kasim Tariq in Uzbekistan.
Remington 700 AICS
A Remington 700 AICS is seen in Division's armory, but never used in the show.
Unidentified sniper rifles
Launchers
RPG-NH-75
Michael (Shane West) uses an RPG-NH-75 during the Chile mission in "Dark Matter" (S1E10) when he destroys a guerrilla-owned truck.
Others
X25 Taser
Seen in episode 7 when Alex takes a X25 Taser from Robby's holster and fires it to stun him before she takes him down.
M18 Claymore
Nikita uses a Claymore to intimidate Russian mafia leaders relaxing in a sauna.