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 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 Vektor R4 modified for the Designated Marksman role when he joins the French Foreign Legion that he uses throughout the film. This weapon would be accurate for the Bosnian Serb military which purchased a few thousand R4 rifles during the conflict, but not for the French Foreign Legion. The modifications include a scope mounted on an AK-style receiver mount (the original Galil scope mount notch was replaced by a lightening cut on the R4) along with a cheek rest which has been installed on the original folding stock and removal of the sights.
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 Bosnian Serb, Bosniak, and Croatian soldiers throughout the film. Peter Dominic also is armed with a Zastava M70AB2.
M16A2
Marine Security Guards at the US Embassy in Paris are armed with M16A2 Rifles.
Submachine Guns
Heckler & Koch MP5A2
The MP5A2 is used in the film by the Bosnian Serb soldier Goran (Sergej Trifunovic).
Machine Guns
Zastava M53
The Zastava M53 (Yugoslavian version of the MG42) is seen in Peter's MG Nest. While there are no definitive features to definitively say this is an M53, the film was shot in Montenegro, were it would be reasonable that it's a locally available M53.
PK Machine Gun
A UN peacekeeper can briefly be seen manning a PK Machine Gun at the prisoner exchange.
During the prisoner exchange a Bosnian Serb soldier is seen with a pump action shotgun, however it is seen too briefly and is too blurred to be worthy of documentation in IMFDB.