For example, setting up event delegation on enhanced elements is best done in the HEAD before the elements load. If you setup all your user-event listeners in the bottom of BODY then your users will have a short time when they'll be interacting with elements which A) will do the non-enhanced behaviour B) do nothing whatsoever. Neither A nor B is ideal.
Google Analytics is generally the only JS I put in the head. If some code is absolutely required for the page to work though then it may make sense to put it ahead of the content.