A bi-tone Heckler & Koch USP was used by Daniel Graystone and the Zoe Avatar in the U-87 Cylon body in Season One, Episode Seven, "Ghosts in the Machine."
Walther P38
In Season One, Episode Seven, "Ghosts in the Machine", Heracles is seen carrying a Walther P-38 into New Cap City. Joseph Adama calls it a "small gun."
Colt Python
A pair of Colt Python revolvers (.357 Magnum) are carried by Joseph Adama and Emmanuelle into the burlesque club in Season One, Episode Seven, "Ghosts in the Machine."
Submachine Guns
MP-40
Kimel AP-9
The AP-9 is often mistaken for the Intratec Tec-9 and its clones (and uses the same magazine). The angled magazine well and sighting system are the giveaways here.
KGP-9
A Hungarian KGP-9 (9x19 Parabellum) being repeatedly stripped and re-assembled by the Zoe Avatar in the U-87 Cylon body in Season One, Episode Seven, "Ghosts in the Machine." It has been dressed up by the show's armorers to resemble a weapon consistent with the Cylon design aesthetic.
Assault Rifles
SA-80
An SA-80 can be seen in the hands of a Caprican police officer at the memorial to the maglev bombing in the Season One, Episode One, "Rebirth." The SA-80 was previously shown in Battlestar Galactica to be the standard-issue assault rifle of the Colonial Armed Forces with SA-80s being seen in the hands of a Colonial Fleet honour guard at Zak Adama's funeral in Season 1 and in the hands of Samuel Anders' resistance fighters on Caprica in Season 2.