There are not very many... the whole point of a mod is to change the general features.
Ultimate Strategies Mod
Adds numerous new formations and strategies for use, whilst making no changes to technologies, etc. at all.
Fyron's Quadrant Mod
Makes massive changes to the maps of the game, but no changes to the technologies, etc.
Krsqk System Mod
Like FQM, makes changes to the maps but not the technologies.
Devnull Mod
Makes minor changes to technologies and such in the interests of balance and AI useability. Very similar to stock in most ways.
Pirates and Nomads
This mod makes a few semi-radical changes to technologies, but is somewhat similar to stock...