1) I flinched BIG time during the scourging scene in The Passion of Christ, where the scource is whipped with so much force, that the shards get stuck deep into the side of Jesus's rib cage, the roman soldier pulls back, realizes its stuck and then yanks it with even more force, just ripping out a chunk. <shudder>
2) Saving Private Ryan, knife scene mentioned above, it is eerie, because I bet every viewer suddenly feels helpless like that that knife is piercing them and they cant do anything about it. It's like for a minute you switch roles with the character and can feel the pain and the helplessness is overwhelming.