As the first implementers of this new genre of technology, we get to decide on a highlighting scheme for the ages:
If highlighting schemes are standardized from the beginning, students will wind up with annotated study guides that they can go back to throughout the rest of their academic careers.
Here's what I i use in my personal study:
Blue - for Things to Be Noted
Yellow - for Main Points
Green - Vocabulary
Pink - Extraodinary point; favorite quotation for personal use
Purple -- book or author to follow up on
Plus, haven't you ever looked through a book you read years ago and been surprised at what you thought was cool enough to highlight? Think what that experience will be for kids and their e-books.
Let's start from this scheme and see what we can come up with.