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.
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).
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.
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.
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.
The advanced HK G11 is the standard weapon of the elite JSSDF commandos who invade Nerv HQ in End of Evangelion. A major feature of the HK G11 is that it fires caseless ammunition. Notice that when JSSDF soldiers fire their HK G11s in the movie, they never expel spent shell casings.
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.
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.
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.
