The Beretta-pistols seen in the Mosque shooting scene are presumed to be of the M9 model, since both Joshua Rose/Guy (Dennis Quaid) and Peter Dominic (Stellan Skarsgard) are US Marine officers and thus having the right to carry them. A Beretta 92FS is also seen in the hands of the wounded muslim who is shot.
Heckler & Koch G3A3
Heckler & Koch G3A3s can be seen in the hands of the Foreign Legion recruits in the beginning of the movie. UN soldiers are also armed with Heckler & Koch G3A3s at the prisoner exchange and at Split.
Vektor R4
Guy is trained on a Sniper Adapted Vektor R4 when he joins the French Foreign Legion that he uses throughout the film. The modifications include a Scope along with a Cheek Rest which has been installed on the original folding stock and removal of the sights.
M53
The M53 (Yugoslavian MG42) is seen in Peter's MG Nest. There are no definitive features to definitively say this is an MG42, However being that filming was in Montenegro it would be reasonable that an M53 is what they were able to acquire locally.
Heckler & Koch MP5A2
The MP5A2 is used in the film by the Serbian soldier Goran(Sergej Trifunovic).
Zastava M59/66
The movie takes place in Bosnia during the Yugoslavian Civil War, and thus many Yugoslavian or possibly Russian weapons can be seen in the movie. Some of the militias appear to be armed with the Zastava M59/66 rifle (local copy of the SKS rifle).
Zastava M70AB2
The Zastava M70AB2 rifles are used by Serbian, Bosnian, and Croatian Soldiers throughout the film. Peter Dominic also is armed with a Zastava M70AB2.