Not an ebook reader per se, but goodreader on iOS is by far the best pdf note taking app around. Not only does it have a gamut of styles of highlighting, but then you can export the whole mess and it makes for a wonderful synopsis of a book, complete with page references.

I have yet to see an effective use of an e-book for books that are meant to be reread not from front to back but by chapters...

Examples would be technical books and philosophy books.