Hi!
I have 2 suggestions based on the need to maintain custom places for script on the site.

There would be a section to add meta information such as data, name, property, etc., this would make it easier to keep things such as Facebooks microdata, alexaVerify, msvalidate, and more.

Then there is additions to the ending body tag such as the rDF markup I have installed could for sure use a place to remain on the page. Currently I have to add a hidden div every update to the bottom of the index

Ok maybe a third. A section to add code to your wonderful check for such things as conversion tracking code. It only fires when a transaction has been completed.

These would be so amazing to have in any template. What makes me actually request it here is, you update your templates pretty regular and it overwrites these changes.

Thanks for the suggestions. We will surely consider them in future depending on possibilities.