The following fireaarms were seen in the anime franchise Neon Genesis Evangelion, including the original 26 episode television series and the finale movie The End of Evangelion:
The standard issue sidearm for all Nerv personnel is the Glock 17. Hyuga retrieves a Glock 17 from his desk when the JSSDF starts to invade Nerv HQ, but like most Nerv personnel, he has no weapons experience beyond basic training, so he nervously checks it by saying "safety off" aloud to himself. Since the Glock 17 has no external safety, it's curious as to how he accomplished this. The answer may be that it is one of the End of Evangelion English dub translation's notorious script problems: The original Japanese version apparently doesn't have Hyuga say an equivalent line to this (unless there's an outside chance he mutters it under his breath) and it appears that the English dub just added in "safety off" to match his lip-flaps when he was talking.
Browning Hi-Power
The Browning Hi-Power is the standard-issue sidearm used by JSSDF commandos.
Heckler & Koch USP
Major Misato Katsuragi's gun is the HK USP. Unlike most Nerv personnel she does not use the standard issue Glock 17, possibly because she is head of the Tactical division. She brandishes it several times during the series. Note that Misato's USP has a rubber grip on the handle. She fires 10 rounds in succession when fighting the JSSDF soldiers. All three of the main H&K USP variants carry more than 10 rounds per magazine, so there is no on-screen evidence establishing which kind she uses (According to Evangelion Chronicle #13, her USP is a .45 ACP variant).
R-92 Revolver
During End of Evangelion, Ritsuko uses a R-92 revolver. Ritsuko conceals her R-92 in her lab coat during her confrontation with Gendo, though there is no indication that she normally carries the gun with her.
CZ-75B
Gendo Ikari pulls a CZ-75B on Ritsuko during their final confrontation. There is no indication that Gendo normally carries a gun with himself, and he may have just been carrying it because Nerv HQ was being invaded by the JSSDF.
Sub-Machine Guns
Heckler & Koch MP5A3
Only briefly seen in episode 23, the Nerv HazMat team seems to be armed with H&K MP5s, probably the MP5A3 variant.
Steyr MPi 69
Nerv's security guards use the Steyr MPi 69 as their standard-issue weapon. While normally only Nerv security guards are armed with Steyr MPi 69's and normal technicians and computer operators are only armed with Glock 17's, command center computer operator Lt. Aoba either manages to get his hands on one or kept one stored in his desk for just such an eventuality.
Assault Rifle
Heckler & Koch G11
The advanced HK G11 is the standard weapon of the elite JSSDF commandos who invade Nerv HQ in End of Evangelion. While the G11 program never really caught on and is now considered defunct, it would have been considered "futuristic" in 1997 when End of Evangelion was made. It was an advanced prototype in the 1990's, so at the time it was a reasonable prediction that weapons design might lean this way by 2015. A major feature of the HK G11 is that it fires caseless ammunition. Notice that when JSSDF soldiers fire their HK G11's in the movie, they never expel spent shell casings.
Other Weapons
Flame Thrower
A JSSDF soldier uses a flame thrower to flush-out and kill Nerv personnel.
Panzerfaust 3
JSSDF soldiers uses Panzerfaust 3s while infiltrating Nerv headquarters.