Russell (David Meunier) is also seen using a Beretta Px4 Storm when the New Bern and Jericho militias simultaneously capture Goetz (D.B. Sweeney) in "Termination for Cause" (S2E05).
Glock 19
In "Oversight" (S2E04), Goetz (D.B. Sweeney) and his Ravenwood mercenaries are seen using Glock 19s with extended 33-round magazines when they attack Stanley's farm.
Heckler & Koch USP
Chavez (Chris Kramer), one of Hawkins' CIA friends involved in Project Red Ball, is seen using a full-size Heckler & Koch USP when he confronts Hawkins in Season 2's premiere "Reconstruction" (S2E01). After Darcy sneaks up on him, Hawkins takes the gun from him, but later gives it back. It's most likely the 9x19mm version, judging by the size of the bore in the third screencap below.
M1911A1
Colt M1911A1-type pistols briefly in the hands of Republic of Texas troopers at their consulate in Cheyenne.
Rifles
M16A1 (with M16A2 handguards)
In what appears to be a continuity error, Jake goes from using an M16A2 in the Season 1 finale "Why We Fight" to using an M16A1 fitted with M16A2-style handguards in Season 2's premiere "Reconstruction" (S2E01).
Colt M16A2
The M16A2 is used by several of Jericho's citizens.
Colt M16A4
The M16A4 is also used in many episodes, mostly by Major Beck's soldiers.
FN SCAR
An FN SCAR-L was seen briefly in "Termination for Cause" (S2E05). It was not seen fired or shown very prominently, suggesting it was probably an airsoft replica.
M1 Garand
M1 Garand rifles are used by an A.S.M.C. honor guard detail in "Condor" (S2E02) and seen in the hands of Eric Green in "Termination for Cause" (S2E05) as well as in "Patriots and Tyrants" (S2E10).
Winchester Model 70 rifles appear in several episodes in the hands of Jericho's citizens.
Carbines
M4A1 Carbine
The M4A1 carbine also is used throughout the series.
Tokyo Marui M4A1 S-System
A few of Beck's men can be seen armed with M4A1s fitted with A.R.M.S. Selective Integrated Rail handguards and folding front sights. Since they are never fired, it's likely they are Tokyo Marui M4A1 S-System or similar airsoft rifles.
Shotguns
Winchester Model 1912
Stanley's sister Bonnie uses the Winchester Model 1912 when Goetz and Ravenwood attack her home looking for the ledger in "Oversight" (S2E04).
Machine Guns
Browning M2HB
A Browning M2HB is seen on the fake M1 Abrams (actually a visually modified British Chieftain tank, also seen in Jarhead) in Season 2's premiere "Reconstruction" (S2E01).
FN MAG
The machine gun seen on the Abrams appears to be an FN MAG (used as a substitute for the M240) in Season 2's premiere "Reconstruction" (S2E01). FN MAG machine guns are also mounted on military humvees in "Jennings & Rall" (S2E03).
Other
M203 Grenade Launcher
An AS Army soldier outside the Texas consulate is armed with an M203 grenade launcher mounted on an M16A2 in the series finale "Patriots and Tyrants".