bEz's code might work, but I think it makes more sense to do it this way:
Code:
// see manual for this style constructor, under DataMapper Models
$term = new Term($term_id);
$user = new User($user_id);
$courses = $u->course->where_related($term);
This will load all courses for a particular user, where they are also related to a specific term. Alternatively, and this really is the same thing, you could do this:
Code:
$courses = new Course();
$courses->where_related($user)->where_related($term);
Don't forget you can add other query options to your search, as well.