For me, it's a fairly obvious one- Live Organ Transplants from Monty Python's Meaning of Life. The whole thing is really just Terry Gilliam madness, but it just freaks me out. Thank God it's followed by the lovely Galaxy Song, though. I don't know if I'd count the whole Mr Creosote sketch because that's just flat-out disgusting... ok, bit disturbing, but more gross than disturbing.
Any other scenes from an otherwise non-horror film that creep you out?