The espionage system in Imperium Galactica 2 was one of the better ones I have come across. It was nice and simple but also effective. You could have up to 12 spies each requiring a spy base building. They had levels and stats and that affected their success rate on missions of increasing difficulty, from acquiring empire info, sabotaging ships and assassinating leaders.
This was similar to what was done in Master of Orion (especially the remake).
I'll have give that game a try, but in addition to espionage and gaining intel, it also adds a whole new level of diplomacy.
Basically, in the remake of Master of Orion, if you capture a spy, you can either let them go free, imprison them (which creates a nice bargaining chip in that the spy's empire might trade for the spy's freedom), or you can execute them which damages your relations with the spy's empire! A very unique way of diplomacy.