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There s a very good write-up of the Mods available for JA2 on RockPaperShotgun

Go read oh people what like JA2...although most will probably already know all about them..
While a good introductory one, it does leave out a lot of mods, like Renegade Republik, Fight For Freedom, Legion 2, Vengeance and AIMNAS to name a few. This link at the Bear's Pit has a longer list, though not sure how updated it is.