Here's a list of links to topics with mods, as far as I can tell. Many were programmed for previous versions. Fortunately, LCS generally works off the .exe file, and the mods change the .exe file. Therefore, most should be installable over current versions of the game. Your traction will vary.
Please add any mods I miss!
Thrown Weapons Mod (Should be current):
http://www.bay12forums.com/smf/index.php?topic=74743.0This mod adds thrown weapons that DON'T explode and kill your squad. I haven't tested it yet.
Arsenal Mod (Version 4.01.4 I think, REQUIRES CODE ADDING SKILL TO IMPLEMENT):
http://www.bay12forums.com/smf/index.php?topic=58596.0This mod adds many more weapons. I don't know how to edit or compile code, so haven't tested it. In theory, one can just add the code from this topic into the game's code, and Viola! More weapons! Lots more weapons!
Stalinist Comrade Squad (Shortly before the game went to 4.0):
http://www.bay12forums.com/smf/index.php?topic=47525.15This mod adds the Stalinist Comrade Squad as new foes! Unfortunately, this version of LCS (not the mod's fault), included the failed attempt at the "public tolerance of violence" issue. In theory, the determination of "Rampage" vs. "Strike" would be based on the public's tolerance for violence compared to the activites of the squad. In reality, it made the game far too unpredicatable. Stalinists will definitely affect the issued "behind the scenes", but due to lacks in the programing, the Stalinists will be hard if not impossible to directly attack.
NO LONGER UPLOADEDExtremely Easy/Hard Edit (LCS version 4.04.1 I think):
http://www.bay12forums.com/smf/index.php?topic=46637.45Pick option 5 at the end, and you can chose whether to use a founder of superness, or a cripple of minimal stats.
I didn't program any of these mods. Hopefully, a catalogue of mods will both allow the updating of mods of interest, and encourage future moding.