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.
Glock 17
The Glock 17 pistol is seen as the primary firearm carried by NERV personnel.
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).
Inglis Hi-Power
The Inglis Hi-Power is the standard-issue sidearm used by Japanese Strategic Self-Defense Force commandos. It can be identified as such by its distinctive rear sight.
Revolvers
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.
Sub-Machine Guns
Heckler & Koch MP5
Only briefly seen in episode 23, the Nerv HazMat team appear to be armed with Heckler & Koch MP5s.
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 69s 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.
Hybrid MPi 69
According to Evangelion Chronicle #22, Aoba's own MPi 69 is a hybrid submachine gun consisting of parts from the MPi and the Russian AEK-919.
Assault Rifle
Heckler & Koch G11
The advanced H&K G11 is the standard weapon of the elite JSSDF commandos who invade Nerv HQ in End of Evangelion. The G11's caseless ammunition is accurately depicted, as the JSSDF's G11s never eject casings (as opposed to their Hi-Powers, which do).
Machine Guns
Gryazev-Shipunov GSh-30-1
Gryazev-Shipunov GSh-30-1 machine guns are seen mounted on United Nations Air Force Sukhoi Su-33 Flanker-Ds in "Asuka Strikes".
MAS NF-1
The MAS NF-1, which is a variant of the AA-52 machine gun mounted on French-made military vehicles, is seen mounted in a co-axial position on JSSDF AMX-10RCs as they lay a bombardment on Nerv HQ in the beginning of End of Evangelion.
Sumitomo M2
United Nations Army and JSSDF Mitsubishi Type 74 MBTs are armed with the Sumitomo M2, the licensed-made version of the Browning M2 as the secondary weapon.
Sumitomo Type 74
The Sumitomo Type 74, the co-axial machine gun version of the Sumitomo Type 62 GPMG, is mounted on Type 74 MBTs in a co-axial position.
Rocket Launchers
M269 Launcher Loader Module
M269 Modules mounted on UN Army-controlled MLRS are used to fire M26 rockets at Sachiel when it begins to approach Tokyo-3 in the first episode. JSSDF-maned MLRS use them in End of Evangelion when they take on Asuka's Unit 02.