If you have the most current version of iBooks and iOS, you can now highlight text in iBooks using several different colors. Think about highlighting a main idea in one color, and then highlighting supporting evidence to that idea in another. Or, consider doing this for character development. Then, when you tap on the "Table of Contents" .. you have a great set of study notes!!
Did you also know that it is now possible to select a passage of text and have the iPad read to you? This works on web pages, in iBooks, and anywhere you can select text!! To activate the Speak Text feature on your iPad, tap on Settings > General > ... scroll down to Accessibility, and turn on "Speak Selection." (If you don't have this option, be sure you have updated your iPad ... you will be prompted to update when you sync in iTunes).