My favourite was Star Wars Rebellion.
That is what I was about to say. Just wish I played it more. Only reason I couldn't play it, was when you paused the game, you can't issue any orders or build orders for your planets. I am just not capable of playing RTS games.
I liked the taking control of a system, building units, and then using the special units to do diplomatic or espionage missions to sway a planet or see what was happening there. The ship battles were rudimentary compared to today but fun to watch.
More than once my spies found a system with 6 imperial units on it that was way over to the rebellion side in influence and one little sabotage mission against one of those units would put that planet into a civil war.
Edited by Sergovan