This file usually contains links to the wordpress website, links to your RSS and comments RSS, and links to the theme creator if you are using a custom theme. Unless you have a good reason to change these things, it is usually a good idea to keep them intact, even if you add more code above and below it.
Like the header, changes made to the footer only apply to the theme who's folder you are working in. If you activate a different theme, the changes will no longer be applied to your blog.
