All of the soldiers in the movie use SIG-Sauer P226R (rail-frame) pistols as their sidearms. Emil Blonsky (Tim Roth) uses his to shoot at Hulk and threaten Dr. Sterns AKA Mr. Blue.
Beretta 92F
The Beretta 92FS is used by many of the New York City police officers during the final battle between Hulk and the Abomination.
Glock 17
Glock 17s are also used by some of the New York City police officers.
Smith & Wesson Model 10 .38 Special Military & Police
In the alternate opening of the movie, Bruce Banner (Edward Norton) walks on top of a glacier, and pulls out an older Smith & Wesson Model 10 revolver. He aims the gun and cocks the hammer, only to transform into the Hulk, and crush the gun in his hand.
This early Model 10 appears to have had the standard 4-inch barrel cut down to about 3-inches.
Submachine Guns
Heckler & Koch MP5A3
Emil Blonsky's (Tim Roth's) weapon during the commando operations is a heavily modified Heckler & Koch MP5A3, fitted with a tri-rail and a Surefire flashlight with a IR filter and cover. Apparently this and the other strike team with Blonsky had tranquilizer ammo in their magazines before switching to live ammo (in the movie's universe, apparently they can swap between tranq and live ammo without modifying the weapon externally in any way).
A Heckler & Koch UMP is used by one of the commandos. It has a straight magazine, so it's either the .40 S&W or the .45 ACP model.
Assault Rifles
M16A2/A4
Nearly all of the U.S. military personnel in the movie use M16A2 and M16A4 assault rifles, and mostly the latter. A close inspection of many of the rifles reveals that they have the removable carry handles (which have been left on in the movie), which means they're M16A4s.
M4A1
M4A1 carbines are also used by the U.S. military personnel in the movie, and by one of the commandos in Brazil. During the shootout at the university, Blonsky briefly grabs an M4 dropped by one of the soldiers and empties it at Hulk futilely. All of the M4s in the movie seem to have the older-style stocks even though the 6-position stock is much more common today.
SIG SG-552
At least one of the commandos in the first battle with Hulk wields a tricked-out SIG SG-552.
Note: The actor playing this particular commando is Al Vrkljan, who was also one of the movie's armorers. Mr. Vrkljan has also posted on IMFDB and provided much of the info on particular types of weapons seen here, for which IMFDB is extremely grateful!
Machine guns
M240B
During the battle at the university, an M240B general-purpose machine gun is fired at Hulk by one of the soldiers.
Browning M2
The Browning M2 heavy machine gun is mounted on Humvees in the film.
GE M134 Minigun
An M134 Minigun is mounted in the doorway of the CH-53 helicopter and fired at the Abomination unsuccessfully.
Sniper Rifle
Steyr HS.50
A .50 BMG Steyr HS.50 long-range rifle is used by a military sniper to fire a tranquilizer dart at Bruce Banner in New York City.
Heavy Weapons
Milkor MGL multi-shot grenade launcher
Some of the soldiers in the movie use Milkor MGL multi-shot grenade launchers to fire at Hulk, including Emil Blonsky.
Unknown (fake?) rocket launcher
The soldiers who are chasing the Abomination, realizing the futility of firing at him with their M16s, grab an anti-tank rocket launcher from the back of their Humvee, but this also proves useless, because the Abomination grabs the rocket from the air. The launcher does not appear to be based on any type of existing weapon, and was most likely a prop fabricated almost completely from scratch. Just looking at it one can come to the conclusion that this piece is fake.