Of all of my recommended changes in the gradebook to make is usable for teachers and students, none do I feel more passionately about than this one.
When an item is in the gradebook but has not yet been marked, it does NOT mean that the teacher wants it treated as a zero. It usually just means that the due date has not come, or if it has, that the teacher has not yet marked it. If the teacher wants it to be counted as a zero (normally because it did not come in), they can give it that mark of zero at the appropriate time. In the mean time, just compute the overall grade with everything that has been marked.
With previous versions of Moodle, we needed to move things in and out of unweighted categories to give the inuititve results. Even with the new version, if this default changes, we will need to expect every teacher to get the customary setting right, not only for their course, but as they create every category. And the lock, hide, unlock cycle will not be an option, but somewhat of a requirement.
Pleeeezzzz, before 1.9 ships. Change line var $aggregateonlygraded = 0; in lib/brade/grade_category.php to
var $aggregateonlygraded = 1;