We recently set up a WordPress site for the New House Basketball Club in Sittingbourne and we used a theme from iThemes as the basis for the design. Quite a bit of CSS had to be changed to get it exactly how we wanted it so we used the Theme Companion plugin for WordPress to override the bits of CSS that we wanted to alter.
Normally we’d use a Child Theme instead of this plugin, but for themes that don’t support Child Themes, Theme Companion can be quite useful.
On the basketball club site, we had to make alterations like increasing the height of the header and logo area and ‘push down’ the top horizontal menu to compensate for the new height. Here is a sample of what we used to acheive this in the Theme Companion editor:
This setup achieves what we want and we didn’t have to edit the original theme files to do it. When there is an update for the theme we can safely overwrite the CSS files without losing our changes.
UPDATE: This plugin seems to have been superseded by the JetPack plugin > CSS Editor. http://wordpress.org/extend/plugins/jetpack/