I cried a bit during the Crucifixion scenes in "Passion of the Christ". I also flinched at the scourging scenes, but not because of the violence. Rather, it's because had Jesus not come, that punishment would've been mine to bear.
I'm weird. I wont cry at sad moments, sure I'll get choked up but I wont cry. But moments like, Ralph deserting Leo in TMNT and then going to Splinter, mad and throwing stuff around....that made me shed a tear.
I don't know what it is about cartoons that just get to me.