At least 2 SIG-Sauer P226 pistols are seen in Season 1 in the case that was in the possession of Deputy US Marshal Edward Mars (Fredric Lane). The pistols are seen used by several of the characters throughout the season. In "There's No Place Like Home, Part 1" (S4E12), Kate is armed with one.
Beretta 92FS
The Beretta 92FS is also a prominent weapon used in the series.
Jericho 941
In "There's No Place Like Home, Part 3" (S4E14), Kate keeps a Jericho 941 "Baby Eagle" in her home that she takes out when she senses that someone is in Aaron's room.
Glock 17
In "The Economist" (S4E03), Sayid is seen pulling a Glock 17 in a confrontation with Elsa. This Glock appears to have the Lasermax built-in sight.
Glock 17 (Stainless Slide)
In "The Economist" (S4E03), Elsa is seen pulling the stainless slide Glock 17.
Walther P38
Walther P38s are seen multiple times over the course of the series. In "The Beginning of the End", Juliet (Elizabeth Mitchell) takes a Walther P38 at the beach camp and carries it throughout the season. In "Something Nice Back Home", Juliet gives a P38 to Jin (Daniel Dae Kim) when he treks to The Staff station. In "There's No Place Like Home, Part 2" (S4E13), Richard (Nestor Carbonell) shoots Keamy (Kevin Durand) in the back with a P38. Please refer to the Discussion section for a more detailed listing of the P38's use in Seasons 2-6.
Walther P99
In "The Economist" (S4E03), Sayid is seen pulling what appears to be a Walther P99 during a confrontation on the golf course.
Shotguns
Remington 870
In Season 4's "The Shape of Things to Come" (S4E09), Benjamin Linus (Michael Emerson) takes from a piano bench an 870 with a pistol grip and shortened barrel when Martin Keamy's mercenaries storm his camp. These shotguns are also seen inside Swan Station's armory.
The Remington 7400 rifle is one of the rifles carried by Richard's men throughout Season 4.
Battle Rifles
M1 Garand
The M1 Garand is seen in the later episodes when used by the Others on the island. Sawyer also uses one.
M1A
An M1A is seen carried over the shoulder of an Other.
SKS
The SKS rifle is used by Sayid in raiding the Others camp in one episode.
Enfield L1A1
In Season 4's "There's No Place Like Home, Part 1", Sawyer is seen carrying the L1A1, which is the British-made variant of the FN FAL made by Enfield. He is seen with it until it's thrown from the helicopter as he bails out.
M4A1 Carbine SOPMOD
The M4A1 SOPMOD is carried by Martin Keamy and the mercenaries who attack the island in Season 4's "There's No Place Like Home, Part 1" and "There's No Place Like Home, Part 2". Most of the M4's are fitted with scopes, sound suppressors and foregrips. Although never used, Sayid can also be seen carrying one after the Mercenaries were killed off before getting on to the chopper.
M1 Carbine
The M1 Carbine is another one of the common weapons used on the island.
Submachine Guns
Heckler & Koch MP5A2
The Heckler & Koch MP5A2 is used by Martin Keamy (Kevin Durand) and the mercenaries, notably to shoot skeet on boat. Note the ambidextrous MP5-Navy trigger group.
Heavy Weapons
M203 Grenade Launcher
An M203 Grenade Launcher is seen mounted underneath Martin Keamy's M4A1 notably seen in Season 4's "There's No Place Like Home, Part 2".
M141 SMAW-D
When Keamy and his mercenaries are seen loading their weapons on the helicopter in Season 4's "Cabin Fever", among the weapons seen is an M141 SMAW-D.
FIM-92A Stinger
An FIM-92A Stinger is also seen among the weapons loaded in Season 4's "Cabin Fever".
M72A2 LAW
M72A2 LAW's are also seen among the weapons loaded in Season 4's "Cabin Fever".