Nearly all of the special forces commandos led by Lieutenant Colonel Austin Travis (Steven Seagal) carry Heckler & Koch MP5A3 sub-machine guns as their primary weapons throughout the movie. The MP5A3s used by the commandos all have the Navy lower receivers and threaded barrels fitted with detachable suppressors of some type.
Captain Rat (John Leguizamo) is the only one of Colonel Travis' men who carries a Heckler & Koch MP5SD3, the integrally suppressed version of the MP5A3. Like the other commandos' MP5A3s, his gun has the Navy lower receiver.
Lt. Colonel Austin Travis (Steven Seagal) carries a Heckler & Koch MP5K fitted with a PDW folding stock during the opening scene at the Chechen safehouse. His gun is not a factory MP5K-PDW because it has the SEF lower receiver (the factory PDW has a Navy lower) and seems to have a fake suppressor welded onto the end of the muzzle (rather than the extended, threaded barrel of the factory MP5K-PDW). This means his gun is a standard MP5K mocked up to resemble an MP5K-PDW.
When Al Sayed Jaffa is kidnapped in Cyprus, one of the British agents who gets killed in the shootout is armed with a strange-looking Heckler & Koch MP5 variant that has a distinctive square-shaped flash hider fitted on the end of the barrel, an MP5SD-type hand guard, and a stockless buttcap. This custom MP5 was originally built by Cinema Weaponry for the Albert Pyun movie Nemesis and would later be seen used in Demolition Man.
It's interesting to note that Hassan is the only terrorist on Flight 343 to use a Skorpion. However, when the commandos are using cameras to look into the 747's cabin and IDing the terrorists' armaments and locations, Baker (Whip Hubley) identified forward cabin guard's rifle as a Skorpion and Captain Rat (John Leguizamo) claims the four terrorists in the main cabin are armed with Skorpions, AKMs and FN FNCs. (Leguizamo also mis-identifies the Skorpions' calibers as 9mm, rather than .32 ACP). This is in spite of the fact that the terrorists they are looking at all clearly have AKMS rifles, and the fact that Grant (Kurt Russell) actually types "AKM" for the forward cabin notes into his computer and "Skorpion/9mm, AKM/FNC" for the main cabin, despite not being able to see the hijackers!
Heckler & Koch USP (mocked up as Heckler & Koch Mark 23)
Dr. David Grant (Kurt Russell) is seen near the end of the film wielding a .45-caliber Heckler & Koch USP visually modified to resemble the Heckler & Koch Mk 23 Mod 0, fitted with a LAM unit (HK Universal Tactical Light (UTL) or Insight Technology M2 light) and a fake Knight's Armament suppressor. This was done because at the time the movie was made, the only Mark 23s in existence were the military Mk 23 Mod 0 issued to U.S. SOCOM; the commercially-available Mark 23 for non-SOCOM users did not become available until a few years later. Coincidentally, Kurt Russell would become the first actor to handle an actual MK23, on the set of 1998's Soldier.
The British intelligence agents who capture terrorist mastermind Al Sayed Jaffa (Andreas Katsulas) in Cyprus early in the film are armed with Walther PPK pistols with suppressors.
When the hijackers start to take over Flight 343, Nagi Hassan (David Suchet), the leader of the group, goes into the bathroom and unpacks a Glock 19 which has been disassembled and hidden in his camera. He carries the Glock 19 as his sidearm throughout the film and uses it to kill passengers (and even one of his own men) on several occasions. The terrorist who watches over the pilots in the cockpit is also armed with a Glock 19.
All of Colonel Travis' SF commandos carry unknown 1911-type pistols as their sidearms. The exact model is hard to determine. The closest guns they seem to resemble are the Colt Mark IV Series 70 Gold Cup National Match (judging by the grips, which are clearly visible in several scenes), but unlike the factory Gold Cup National Match pistols, they have standard vertical slide serrations (Gold Cups have slanted serrations), as well as ambidextrous extended safety levers. It's quite possible that they were custom-built 1911s assembled by the armorer specifically for this film.
What appears to be a High Standard HDM with adjustable sights is seen in the vest holster of Lt. Colonel Austin Travis during the opening mission to retrieve chemical weapons.
Almost all of the jihadist terrorists in the movie, including the Chechen mafia thugs at the beginning, Al Sayed Jaffa's men in Cyprus, and the Algerian terrorists who hijack Flight 343, are armed with folding-stock AK rifles which may appear to be the AKMS, but a close look reveals that this is not the case - The AK rifles in the movie have the stamped lower receivers, ribbed receiver covers, wider front grips, and slant compensators of the AKM, but they also have the .75" front sight of the AK-47, older-style ventilated gas tubes, and the heavier folding stock (the AKMS has prominent serrations along the arms of its folding stock to reduce weight). In other words, the weapons are a strange mix of AKS-47 and AKMS design details. The most likely explanation is that they are Norinco Type 56-1 rifles which were given the AK-47-style front sight and AKMS grips and receiver covers.
One of the AK-type rifles in the movie does appear to be a genuine AKMS, though it has a side-folding stock similar to that of an SA Vz.58, rather than an under-folding stock. It's probably a regular AKM with the fixed stock removed and the Vz.58 stock fitted by the movie's armorer.
When the commandos need another shooter to assist in taking control of Flight 343, they ask Dr. David Grant (Kurt Russell) to work with them. Grant is given an Ithaca 37 "Stakeout" short-barrel shotgun for the job.
What appears to be a Chinese Type 69 copy of the RPG-7 is used by one of Al Sayed Jaffa's men when he is kidnapped in Cyprus. The weapon is not seen very clearly for very long, however.
