I was in a Huge map game and had established an alliance with all but one civilization. I proceeded to conquer this last race. With only one planet left in their pocession, they admitted their defeat and turned the planet over to me. Knowing that I had won an alliance victory, I simply hit the "End Turn" button.
Unfortunately, one of my ships that was on autopilot was set to end it's turn in a sector containing one of my ally's ships. A message informing me of this fact appeared so I clicked the "Done" button thinking I would be taken to my ship so I could adjust it's path. Instead, I got into an endless loop of trying to end the turn and getting the warning message about my ship attacking an ally.
I finally had to kill the game through the Windows task manager.
Another one to add to the list.