Gendo Ikari pulls a CZ-75B on Ritsuko during their final confrontation.
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.
Submachine Guns
Nambu Type 100
Seen in Episode 4, Kensuke Aida owns a replica Nambu Type 100 submachine gun.
Heckler & Koch MP5
Only briefly seen in episode 23, the Nerv HazMat team appear to be armed with Heckler & Koch MP5A3s.
IMI Uzi
Nerv's security guards use the IMI Uzi as their standard-issue weapon.
Hybrid Submachine Gun
According to Evangelion Chronicle #22, Aoba's personal submachine gun is a hybrid consisting of parts from a Steyr MPi 69 and the Russian AEK-919K Kashtan. While normally only Nerv security guards are armed with submachine guns and normal technicians and computer operators are only armed with Glock 17s, 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.
Rifles
Dragunov SVD
Briefly seen in Episode 4, Kensuke Aida owns a replica Dragunov SVD, which he keeps in his tent.
Heckler & Koch G11
The advanced Heckler & Koch 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); its reciprocating magazine, on the other hand, is not.
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.
A JSSDF soldier uses a M2 Flame Thrower to flush-out and kill Nerv personnel.
Evangelion Weapons
The Evangelions (or simply Evas), the massive humanoid constructs around which much of the story's plot centers, use a variety of weapons; while some are fictional, many are based off of real-world firearms (albeit visually modified, and scaled up to fit the Evas' massive size).
Steyr ACR
The most prominently-featured weapon used by the Evas is a scaled-up Steyr ACR, referred to for unclear reasons as a "Pallet Rifle". It is never shown being reloaded (the Evas simply dropping them when they run out of ammunition), nor is it ever shown ejecting spent casings (implying that, unlike the real ACR, the Pallet Rifles use caseless ammunition of some form); it apparently fires explosive shells, and is shown as being more or less useless in every one of its appearances barring Episode 11.
PTRS-41
A major plot device of Episode 9 is the "Positron Rifle", a prototype energy weapon under development by the JSSDF; it is "requisitioned" by Nerv and rebuilt for Eva use, with the resultant weapon seemingly based on the PTRS-41 anti-tank rifle. Notably, it features a series of cables attached to it (most prominently to a large block where the PTRS's magazine would be); these are plugged into the weapon's power source, which consists of the entire Japanese national grid. The weapon is also used in Episode 22, albeit to considerably lesser effect, and apparently without its national-blackout requirement.
IMI Desert Eagle Mark XIX
In Episode 16, Shinji's Eva Unit-01 is seen using a handgun which appears to be a scaled-up, but otherwise completely unaltered IMI Desert Eagle Mark XIX, right down to the rather baffling inclusion of the scope mounting rails; it is used to little effect against the episode's Angel, and is never seen again (presumably having been lost in the Dirac Sea said Angel created).
Accuracy International Arctic Warfare
Rei's Eva Unit-00 is seen on two occasions (Episodes 16 and 23) with a sniper rifle based on the Accuracy International Arctic Warfare; alongside alterations to the profile of the stock, the most prominent difference between the real rifle and the Eva version is that the latter is semi-automatic.
Unknown Rocket Launcher
Asuka's Eva Unit-02 is seen with an unidentified, possibly-fictional repeating rocket launcher on two occasions (Episodes 18 and 19). In the former, she doesn't ever fire the weapon, while in the latter she dual-wields them; for entirely unclear reasons, this does practically nothing to her target.