The Nook should fill you needs
I'm by no means an expert on ereaders. I just recently purchased a Nook and my wife has a Kindle2. I think a Nook will work for what you are looking for in an ereader. I love mine and in my opinion it's better than the Kindle. You can bookmark, highlight and add a note to the highlighted section as you inquired. My understanding also is that the Nook will work with more ebook formats. Beside B&N is a bookstore so books is their business.