How about The Mission? Dude on a cross going over a waterfall is pretty tough to miss. 
Oh, and more recently, there’s that bit in Life of David Gale where we get an overhead shot of the title martyr lying in the yard with his arms outstretched. Gag.
I feel obliged at this point to quote from an (unproduced) screenplay I co-wrote a long time ago. Steve and the Colonel are pinned down in a firefight against the Mysterious Forces of the Evil Conspiracy when Steve’s hands start bleeding a la stigmata:
STEVE:
Aaaa! I’m hit!
COLONEL:
(firing his pistol wildly)
Lemme see
STEVE SHOWS THE COLONEL HIS BLEEDING HANDS
COLONEL:
You’re not hit. That’s what you call your basic gratuitous Christ imagry.
STEVE:
What does it mean?
COLONEL:
I don’t know, but it doesn’t look good for you.