this is a long shot request, and open to discussion.

when managing project configurations (eg email notification, workflow thersholds)
it would be useful to have individual tristate checkboxes allowing for each option:

• explicit "yes" / "no" to override configuration
• 3rd state meaning "not defined", thus using the default configuration

Other options which are not checkboxes, can also benefit from a "default" option.

From my experience on managing multiple projects and sub-projects, i find most of the times a change implies the need of changing only one small subset of the options available, for a number of projects. However setting at least one change makes the whole option-set to be fixed and separated from main site configurations (all projects).
If a subsequent requieriment ask for any change in site-wide settings (all projects), i would then have to go through each one of the specific project configurations to modify it.