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General Joe Colton (Bruce Willis) uses a custom M1911A1 with ivory grips. In the film it is stated that the pistol belonged to Patton and was a gift from his family. Colton gives it to Roadblock (Dwayne Johnson) at the end of the film.
Glock 21
The Glock 21 appears as the standard sidearm of G.I. Joe. Roadblock (Dwayne Johnson) uses two fitted with detachable magazine housings, built from parts of the TDI Vector.
FN FNX-9
The FNX-9 is used by both Cobra ninjas and Cobra Vipers. Snakes Eyes (Ray Park) and Jinx (Elodie Yung) both take one after they secure Storm Shadow (Byung-hun Lee) in the Himilayas.
FN FNX-45
Firefly (Ray Stevenson) uses two FNP-45 pistols with stainless steel slides as his personal weapons.
Several guards can be seen with Heckler & Koch MP5A2s fitted with Navy trigger groups & Surefire dedicated forend weaponlights.
Heckler & Koch MP7A1
A number of what appear to be Heckler & Koch MP7A1s can be seen mounted on the side of a motorcycle operated by Firefly (Ray Stevenson). Snake Eyes (Ray Park) can also be seen using a suppressed MP7A1 to shoot down incoming shuriken.
Rifles
FN SCAR-H
The FN SCAR-H appears to be the main battle rifle carried by the Joes. It's seen used by Duke (Channing Tatum), Lady Jaye (Adrianne Palicki) and Flint (D.J. Cotrona). They are fitted with various accessories including Aimpoint Micro T-1 red dot sights, Magpul AFG grips, AN/PEQ-15 laser modules, and tactical flashlights.
FN SCAR-L
The FN SCAR-L appears as G.I. Joe's standard carbine. They are fitted with Aimpoint Micro T-1 red dot sights, Magpul AFG grips, AN/PEQ-15 laser modules, Magpul EMags, and occasionally 10.5" barrels to comfotably accomodate suppressors. They can seen in the hands of Duke (Channing Tatum), Lady Jaye (Adrianne Palicki), and General Joseph Colton (Bruce Willis).
Colt M4A1
A few Joes at their camp in Pakistan are seen carrying M4A1carbines. After the Apache air strike, several Cobra Vipers sweeping the camp for survivors are seen with M4A1s as well.
Noveske N4 CQB
A Noveske N4 CQB is held by General Joseph Colton (Bruce Willis) in an international poster and is visible in an armory.
Custom Center Balanced Systems AKM
Customised AKMs fitted in Center Balanced Systems stocks are used by Cobra troopers.
A Browning M2 Aircraft machine gun is being fired handheld by Roadblock. An M2 can also be seen mounted on the the roof of a "Ripsaw" tracked vehicle made by Howe and Howe Technologies, and is presumably the weapon Roadblock is seen wielding as it has the same custom "chainsaw" grip.
Browning M2HB
A Browning M2HB can be seen on a Cobra boat and in a museum.