X3: Terran Conflict. Im probably modding it more than I'm playing it but it's the thought that counts.
Simply the prettiest starship flying game around and moddable (and already modded) beyond recognition. Practically nothing is off-limits for modders. There are new weapons, ships, stations... whole new universes.
And it's the only game where you have a freedom comparable to GalCiv. No other game has the same vertical depth. Trucking around in a trader, mining asteroids, flying a tiny scout, or commandeering a fleet of battleships, carriers, and missile frigates. Anything goes.
And once in a while... Master of Magic, Magic Carpet 2, or Populous 2.