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. CIA analyst Ryan Fletcher (Noah Bean) is armed with this in Chile before he is forced to drop it after being held at gunpoint. Owen takes the P226 from Cleary (Michael Cram), a CIA agent stationed in Chile, on a Hercules C-130 en route to the US. Division security personnel, most notably Robbie (Bug Hall) carry P226's as well. A two-tone P226 is used by Percy in Knightfall to cripple Ramon in order to force him to work for Division.
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.
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. Michael still uses it in the 2nd season, as well as a few gunmen under Dr. Mars in Falling Ash. A few Division operatives use the 92FS in Game Change.
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 and Pandora. In Partners, former Division agent Kelly (Katheryn Winnick) is seen using a PX4 during a confrontation with Alex and Nikita.
Beretta Px4 Storm Compact
Ari Tasarov (Peter Outerbridge) is seen removing a Px4 Storm Compact from Sergei Semak's (Peter J. Lucas) desk. A few moments later, Sergei is seen using it to execute a GOGOL official after questioning him.
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. Ex-Guardian Dana Winters, in a shocking display of skill, uses one in Glass Houses to execute an entire Division strike team in seconds, headshots only. Nikita uses it in Game Change after disarming a mobster.
Glock 17 with a CAA Tactical RONI-G1
A Glock 17 on a mounted 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. In Falling Ash, it's used by a brainwashed ice cream vendor to assassinate a US Senator.
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. She later uses it in Knightfall when aiming it from behind a crippled Ramon in Division's Colombian base. A brainwashed woman in Falling Ash uses one when she was brainwashed to assassinate a Senator.
AMT Backup
Nikita carries an .380 Auto AMT Backup in One Way, and can be seen one Michael forces her to drop all of her weapons.
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 906
Used by Alex to execute her captors after being free 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 episode 17, 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.
Unknown Revolver
Submachine Guns
Calico M950
A brainwashed Alice (Julie McNiven) in Falling Ash is armed with a Calico M950 outfitted with a scope when Dr. Mars plays a music file when Owen instructs him to download files for the Regiment.
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. Al-Qaeda terrorists are seen using MP5A3s with tactical foregrips on.
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. Michael uses one in Game Change.
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 episode 6 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 is armed with a Sterling after engaging Alex and Jaden (Tiffany Hines). It's not clear on the specific type.
Rifles
AKM
Armeanian Border Guard soldiers are armed with the AKMS in Partner.
Colt Law Enforcement Carbine
One of the Divison agents in "343 Walnut Lane" carry Colt Law Enforcement Carbines fitted with a telescopic sight. The weapon has also been modified with a number of Magpul accessories, including replacement base plate on the magazine, a UBR stock and an MOE handguard. The weapon is later picked up and used by Roan (Rob Stewart).
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.
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. 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. Several guards appear to be using them during Robbie's rampage but only the stock is shown clearly, everything else is blocked by weapon lights aimed at the camera.
IMI Compact 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. It's later seen on Trevor's table, fitted with the same accessories. In Falling Ash, Owen uses it as his main weapon when he and Michael raid Dr. Mar's fake therapy clinic. A Division operative uses one in "343 Walnut Lane".
M16A1
Michael (Shane West) uses and M16A1 fitted with an M203 (along with the correct leaf and quadrant sights) in "343 Walnut Lane".
M16A2
M16A2 rifles are used by US Army personnel in Dark Matter.
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 and Covenant. 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 operators. Division operatives sent to kill Nikita and Michael are armed with M4A1s with C-More red dot sights. In a flashback, Roan and a team of Division agents use the rifle while disguised as American soldiers. Roan uses one again in 343 Walnut Lane with an M203 grenade launcher mounted.
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 are seen using them as well. In Knightfall, a flashback shows Division guards standing guard behind Ramon with 552s.
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 fifth episode.
Mossberg 590
Nikita uses a Mossberg 590 when rescuing Jill from Division in S1E3 "Kill Jill"
Valtro PM5
GOGOL operatives carry Valtro PM5 pump-action shotguns with detachable magazines during the forest shootout in Turkey at the end of "Partners" (S2E4).
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.
Sniper Rifles
Accuracy international Arctic Warfare
Seen in Division's armory, but never used in the show.
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.
Ruger 22 Charger
Alex uses a custom Ruger 22 Charger with an extendable buttstock, scope and suppressor in Knightfall.
Rocket Launchers
RPG-22
Michael uses an RPG-22 during the Chile mission when he destroys a guerrilla-owned truck.
Others
Automated Machine Gun
In Partners, an automated machine gun based from an M4-type rifle with a 100-round magazine was used near the Turkey-Armenia border to "shoot" at Nikita.
M18 Claymore
Nikita has Claymores uses to intimidate Russian mafia leaders relaxing in a sauna.
X26 Taser
Seen in episode 7 when Alex takes a X26 Taser from Robby's holster and fires it to stun him before she takes him down.
Cane weapon
Alex was armed with a cane that was actually a firearm in Falling Ash. It was never used since she intervened to save a Senator from being assassinated.