Martin (Jeffrey Pierce) aims his silenced Beretta 92A1 at Nikita in "3.0" before switching to a 3rd generation Glock 17. Nikita takes a 92A1 off a Brazilian ABIN agent in "High-Value Target" (S3E20), and uses it till the end of the episode.
Beretta 92FS
Wade uses a Beretta 92FS as his sidearm in "Innocence". Alex and Owen are armed with 92FS during the raid in Luxembourg in "Consequences". Uzbek bodyguards of Division agent/Uzbek president Alexi Markov are armed with 92FS pistols in "The Sword's Edge". In several continuity errors, Nikita is seen with a 92FS instead of her normal PX4.
Beretta 92FS INOX
Sean continues to use a Beretta 92FS INOX as his sidearm from Season 2. A Secret Service agent is also seen giving Nikita a 92FS INOX in "Til' Death Do Us Part" (S3E22).
Beretta Px4 Storm
Nikita carries the Beretta Px4 Storm INOX as her sidearm, replacing the Walther P99AS from Season 2. Michael uses a regular Px4 Storm in "True Believer" and in "Intersection". One of Ari's GOGOL agents has a Px4 Storm holstered in "Consequences" before Alex uses it to kill him. The Px4 becomes Division's standard pistol in Season 3 and is carried by most characters
Beretta Px4 Storm Sub-Compact
Alex continues to use the Beretta Px4 Storm Sub-Compact as her main sidearm from the previous season.
Glock 17
The Glock 17 is visible in "3.0", carried by Hong Kong-based MSS agents, Hong Kong Police Force uniformed police and Martin. Glock 17s are visible in "True Believer". Nikita uses one after disarming a terrorist in "Sideswipe".
Glock 26
A Glock 26 is used by Eliza Abbot in "Innocence" (E2). Micheal switches to the Glock 26 after being injured in "Intersection" (E7)
Anne (Sarah Allen), a rogue Division agent working under Amanda uses a Stechkin APS in "Consequences".
Zoraki 925
Shop henchmen use Zoraki 925 machine pistols with 25 round magazines in "High-Value Target" (S3E20)
Revolvers
Chiappa Rhino 20DS
Ari Tasarov (Peter Outerbridge) fires a chrome Chiappa Rhino 20DS when his safehouse is raided in "Consequences". For the most part, this revolver is Amanda's weapon of choice in Season 3.
Chiappa Rhino 50DS
Tariq Rafat (Al Bernstein) uses a Chiappa Rhino 50DS in "Sideswipe" with black grips. Cyrus disarms Rafat and uses it in St. Lucia before he discards it.
Smith & Wesson Model 10
What appears to be a Smith & Wesson Model 10 is used by a Third Wave terrorist in "True Believer".
Submachine Guns
Heckler & Koch MP5A3
Hong Kong-based MSS agents in close protection duties use Heckler & Koch MP5A3s in "3.0". Some are outfitted with RIS barrel to allow the use of vertical foregrips. Division agents also use the same weapon.
Heckler & Koch MP5K
Sean uses a Heckler & Koch MP5K when he saves Alex and her Division team from a GOGOL ambush in "Sideswipe". Sean, Owen Niktia, and other Division agents carry the weapon in "Survival Instincts" (S3E9).
Heckler & Koch MP7
Nikita continues to use the Heckler & Koch MP7 as her primary weapon from Season 2, first seen in "Innocence". A few FBI SWAT operators are armed with MP7s in "True Believer", which is wrong since they are not using the weapon in real life. In "Consequences", Division agents are armed with the MP7 aside from the MP5A3 as their main submachine guns. Alex dual wields them in an ambush in "Sideswipe".
Assault Rifles
AKM
Ari's GOGOL agents carry their AKMs with Picatinny railings and modern furniture during the graveyard ambush in "Consequences". Michael uses one in the same episode after taking it from a dead GOGOL agent.
Colt M4A1
FBI SWAT operators carry Colt M4A1s in "True Believer", and the weapon is seen in a Ranger group photo.
Mk. 18 Mod 0
Hong Kong Police Special Duties Unit operators use Mk. 18 Mod 0 rifles in "3.0" (S3E1)
Beretta ARX-160
Michael uses a Beretta ARX-160 as his main assault rifle from Season 2.
IMI Tavor TAR-21
MSS agents in Hong Kong use IMI Tavor TAR-21s as their main assault rifle in close protection duties in "3.0".
Czech Small Arms Sporter Compact
Ari's GOGOL agents also carry the SA vz.58 Compact during the graveyard ambush in "Consequences".
SIG SG 552
Division agents continue to carry the SIG SG 552 in Season 3.
Shotguns
Remington 870
What looks to be a Remington 870 is used by a SDU operator in "3.0". A FBI SWAT operator is armed with a Remington 870 in "True Believer".
Serbu Super Shorty Remington 870 Shotgun
Michael uses the same Serbu Super Shorty from season 2 as his main shotgun.
Sniper Rifles
Kel-Tec SUB-2000
Martin uses a Kel-Tec SUB-2000 rifle in Hong Kong in the episode "3.0" fitted with a railed handguard, suppressor, riflescope and bipod. Alex later uses it after taking it from him.
Blaser R93 Sniper Rifle
The Blaser R93 LRS2 is seen used by Michael in a tower in "Sideswipe".
Machine guns
GE M134 Minigun
A M134 Minigun was used as a machine gun post by ex-Division agent turned arms dealer Cyrus (Isaiah Mustafa) in "Sideswipe".
M60E4
In a Ranger photo in "True Believer", Joshua aka Major Trevis Ryerson is armed with the M60E4 in a pose.