A total conversion mod is one that changes nearly everything about the game, usually to make it resemble some particular genre. The Star Trek Mod is a total conversion mod because it replaces most of the tech tree and all of the races with techs and races from Star Trek. The Fantasy Empires Mod is a total conversion mod for the same reason - it replaces the standard space elements with ones from fantasy (elves, orcs, wizards, etc.) Carrier Battles Mod and Adamant Mod are borderline total conversion mods; they change much of the existing game structure, but do not emulate any particular genre.
Examples of total conversion mods: