I think Distant Worlds has an amazing AI. The game RTS that is so huge that the way you play is to set parameters for the AI and change those parameters based on the events of the game (you can take direct control but it really is not practical with the exception of some small tweaking). It is amazing to be how well the your assisting AI and your opponents AI can manage a game with so many options so well.

I liked the AI of Alpha Centauri. I felt like I could realla relate to the different factions as if they were kind of human and had personality. Also they weren't too stupid for the average player.