The Bear’s Pit forums, as belgerog mentioned, are the hub and lifeblood of Jagged Alliance 2 modding.
http://www.ja-galaxy-forum.com/
Unfortunately, the last time I tried to link to a specific forum thread, it didn’t work for most people (though it worked for me). Here’s the link to the thread with the mod that I’m currently using.
http://www.ja-galaxy-forum.com/board/ubbthreads.php?ubb=showflat&Number=244109&page=1
Bear’s Pit Community -> Forums -> JA2 v1.13 Modders HQ -> v1.13 Mod General Discussion -> Single Click Installers STOMP + HAM + WF + AIM (+NAS)
The hottest new SCIs (single-click installers) seem to be made by Tai, who has his own thread on the same forum. It is also possible to download using SVN and/or combine mods on your own, but that’s pretty power-user. Even the “single-click” installers require some knowledge to use, though the forum users are pretty helpful with technical questions.
Because Bear’s Pit speaks in its own lingo of abbreviations, I’ll break down a few of the mods as I understand them.
v1.13 - the most popular base mod for JA2. It adds a more realistic inventory system, true automatic fire on guns, some balance changes, high-res support (kinda), and various other tweaks. They have rolled HAM (Headrock’s Assorted Modifications) into the base code, which most notably has a system for suppression fire.
AIM - Alpha Item Mod. This one is relatively new and I’m not entirely sure what it does.
NAS - New attachment system. Vanilla JA2 limits each gun to four attachments, this mod creates attachment hardpoints in all the areas that one would realistically expect being able to attach or swap out components, and then some. Attachments are, of course, restricted to hardpoints where they would actually fit, i.e. no silencers hanging off the end of a magazine.
WF - Wildfire. This is a mod that changes maps and mercs from basic JA2. It later went retail, but can still be enjoyed as a mod. It’s not necessarily better, though I like the new maps because they feature more close quarters for ambushing. The main perk is really just having variety when you’ve played the basic JA2 campaign to death.
STOMP - Sandro’s Trait and Other Modifications Project. I cannot bring myself to play Jagged Alliance 2 without this mod anymore (much like 1.13). It revamps the trait and personality systems into more transparent mechanics with greater possible variety and tighter character focus. If you want a character who runs fast, specializes in rifles, and punches people in the face, you can do that. Speaking of which, in conjunction with the traits, it also improves JA2’s close combat (fisticuffs and melee weapons) and AI. Vanilla JA2 close combat is kind of . . . not useful.
All the trait values are externalized into an .ini file, so you can tweak them to your liking as you get a better feel for the game. Personally, I gave close combat specialties a huge defensive buff, since modern soldiers are more likely to have to defend themselves in close quarters than attack with fists and knives. It doesn’t solve the issue of point blank shooting, but nothing’s perfect.
IoV - Don’t know what this mod is either. I haven’t found a version with STOMP, so for me it’s a non-issue atm.
So yeah, it sounds complicated, it is. That said, I truly think most of these mods (except Wildfire) add logical features to JA2 without fundamentally changing its flavor. If you have any questions, Bear Pit and/or myself can probably help.