During the final fight sequence between Spock and Khan. Spock applies the Vulcan nerve pinch to Khan, who lets out a scream of pain but doesn't collapse.
Why didn't the nerve pinch work?
In the original series "Assignment: Earth", the human derived from a hidden planet, Gary Seven, shrugs off a Vulcan nerve pinch without any discomfort at all.
Khan is not incapacitated by it, but does create much pain for him—so presumably it would be worse for anyone else. We don't know if his superior muscularity guards the nerves or if his genetically engineered nervous system is better able to cope with the paralysis effects normal to humans.
Presumably then, the maneuver is most effective on more weakly engineered humans. The most advanced are less affected by it.
Spock's Vulcan Nerve Pinch was much less effective on Khan, due to his superior genetic engineering. Although, it had a temporary painful effect, Khan, as stated in the film, was the most dangerous adversary they have/had ever faced.