See www.w3schools.com/tags/tag_doctype for more information on HTML doctypes.
The default doctype for Confluence 5, and the one used in the ThemeBuilder ROOT theme, is <!DOCTYPE html> . You can change this in a custom skin, but need to be aware that it will change how your pages are interpreted by the browser.
This option allows you to add attributes to the <HTML> tag for all pages viewed with the skin. The primary purpose of this option is to add a VML namespace when using things like the Google Maps API:
Each of the Header, Body and Footer sections has a popup editor that will enable access to write additional HTML into the Header, Body and Footer sections of the current skin.
You will need to click the 'Save' button to apply any changes made in the 'HTML' screen.