Kamuzawa, the head of the Diclonius Research Facility, uses a stainless-steel SIG-Sauer P220.
Desert Eagle Mark VII
In a rare case of justified use of a Desert Eagle, the mercenary Bondo wields two of these .50AE handguns against Lucy (One is kept as a backup weapon). While her vectors can block most handgun rounds, both high-velocity rifle rounds and heavier handgun rounds (such as the .50 Action Express) can pass through her vectors, making this normally ludicrous weapon choice perfectly reasonable.
Unknown Handguns
Utilized by Chief Kurama and a S.A.T. officer.
Unknown Snub-Nosed Revolver
Used by a security guard in the first episode.
Sub-Machine Guns
Heckler & Koch MP5-A4
Both Japanese S.A.T officers and security guards inside the Diclonius research facility use H&K MP5-A4 sub-machine guns. All have a Safe/Semi/Burst/Auto selectors, and a few have dual magazine clamps. This is by far most seen weapon in the anime.
Heckler & Koch MP5A4 with M203 attachment
The borderline psycopathic Bondo uses a H&K MP5-A4 outfitted with a M203 during his initial hunt for the escaped Diclonius. Disappointingly, he only uses the grenade launcher once.
Rifles
FAMAS G2
When one of the Diclonius escapes into the hallways of the S.A.T. research facility, Professor Kakazawa uses a FAMAS G2 to stop her. The Diclonius' vectors are capable of stopping most bullets (such as the 9mm Parabellum used in the guards' MP5s) but cannot stop higher velocity rounds (such as the 5.56 NATO used by the FAMAS) if they are not distinctly aware of the threat.
AW50F
A AW50F is used by a S.A.T sniper against Lucy in a last-ditch attempt to thwart her escape.