As Asad said you can edit the header and footer of the skin by editing the layout.master file of the skin.
However, some skins also have 2 extra content sections and these can be used the same as the 3 columns and can be used for editable header or footer content.
If you try the skins andreasvicklund-02-alt1, i7media-2horizontalmenus, and ramblingsould-5contentpanes. Then you will see more than just 3 columns in the PageLayout.aspx page because it detects these extra content sections.
Hope it helps,