Some themes already feature a separate options page and some of those allow you to enter custom CSS that will override the styles defined in style.css
Why is that great? You can easily change the look of a theme without having to change the style.css itself. When you upgrade the theme, your changes are kept and you don't have to tweak style.css all over again.
It'd be great if WordPress would have such a feature. Just a box that allows you to add custom css that is included after the theme css.