Hi Caroline,
Many (most?) of the moodle2 themes have settings pages which allow varying degrees of customisation. The most comprehensive of these is probably my own flexi_ii theme which you can find in the plugins database, although this may go beyond your needs.
The one issue I can see with any of the themes though is that they offer this customisation for the theme itself and not for each course - if the same theme is used on a number of courses, changes made in the settings for one course would affect every course using that theme. I am not aware of any theme which allows settings on a per course basis.
To get around this, I think you would have to create a clone of the main theme for each course using it - in effect giving them a different theme each so that their settings only apply to that course. Depending on how many courses you have, that could end up being a lot of cloned themes!
Richard