William Stranix (Tommy Lee Jones) uses a Heckler & Koch P7M8 throughout the movie. He holds it high during many scenes, clearly showing the single stack 8 round magazine.
M1911
Several of the terrorists Carry M1911 pistols as well as many of the US Navy officers and Marines.
Casey Ryback (Steven Seagal) also uses a 1911 while swimming next to the Sub to shoot 1 man and then place his bomb.
Beretta Model 92F
Silenced Browning Buckmark .22 Pistol
Sig P226
Uzi
Micro Uzi
MP5K
MP5A3
HK94
Actually some of the "MP5"s are full auto conversions of HK94s. One of the terrorists uses a long barreled HK94 with a 'slip over' fake suppressor to fire.
Steyr AUG
M16
Ingram MAC-10
Cobray M11
Stinger Missile
Rubber guns
During the initial assault many of the terrorists are using obviously rubber weapons. They are cast from the real deal and used in any scene where stunts occur. It is much safer to wave around and hit other actors with rubber guns than the real thing.