In the Season 1 finale "What Kind of Day Has It Been" (S1E22), one of the white supremacists uses a Beretta 92F to open fire on President Bartlet (Martin Sheen).
Beretta 84B
Secret Service Agent Simon Donovan (Mark Harmon) takes what appears to be a Beretta 84B off a convenience store robber in Season 3's finale "Posse Comitatus" (S3E21).
Desert Eagle
In the Season 1 finale "What Kind of Day Has It Been" (S1E22), one of the white supremacists uses a stainless Desert Eagle to open fire on the President.
SIG-Sauer P228
A SIG-Sauer P228 is fired by a Secret Service Agent in the Season 1 finale "What Kind of Day Has It Been" (S1E22), White House Communications Director C.J. Cregg (Allison Janney) mentions in a later episode that the weapon was a SIG-Sauer 229, but the weapon is in reality the 228.
SIG-Sauer P226
US Secret Service Agent Simon Donovan (Mark Harmon) pulls his SIG-Sauer P226 in Season 3's finale "Posse Comitatus" (S3E21).
Smith & Wesson Model 66
A convenience store robber appears to be armed with a Smith & Wesson Model 66 in Season 3's finale "Posse Comitatus" (S3E21).
Smith & Wesson Model 686
In Season 3's "We Killed Yamamoto" (S3E20), US Secret Service Agent Simon Donovan (Mark Harmon) is seen firing a .357 Smith & Wesson Model 686 on the range. When Donovan mentions that it's a .357 Magnum, C.J. Cregg (Allison Janney) mentions that "it's a good brand". She also gets to shoot the revolver, but the recoil puts her on the ground.
Glock 17
A Glock 17 is drawn by Secret Service Agent Wesley (Taye Diggs) in Season 4's "Commencement" (S4E22).
Submachine Guns
Heckler & Koch MP5A3
In Season 2's "In the Shadow of Two Gunmen, Part II" (S2E02), SWAT officers are armed with the Heckler & Koch MP5A3's as they apprehend one of the suspects in the assassination plot against the President. In Season 3's "Posse Comitatus", a Black Ops team is seen using the A3 to take out a foreign defense minister suspected of terrorist activities.
Rifles
M1 Garand
The M1 Garand rifle is seen held by members of a Marine honor guard detail in Season 1's "In Excelsis Deo" (S1E10). A Marine also is seen performing rifle drills with a Garand in Season 1's "Lies, Damn Lies, and Statistics" (S1E20).
M4A1
The M4A1 is used by FBI agents that apprehend the suspect in Season 2's "In the Shadow of Two Gunmen, Part II" (S2E02).