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.
Winchester Model 70 rifle appear in several episodes in the hands of Jericho's citizens.
Rifles
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.
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).
M4A1 Carbine
The M4A1 carbine also is used throughout the series.
Heckler & Koch HK416
The Heckler & Koch HK416 appears to be one of the weapons carried by Beck's men.
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).
M240
A pintle-mounted M240 is also seen on the Abrams in Season 2's premiere "Reconstruction" (S2E01).