NowLedge is a book-focused note taking app that works with PDF files. Read your book like you would do with a PDF Reader, take highlights and add notes in bullet point format. Your notes are displayed nicely in a grid format when needed.
@vivekweb2013 Thanks mate, I built NowLedge for myself first because this was indeed a painful problem I had :)
There is a cost of entry, in the sense that you need to annotate a full book with it before seeing all of the benefits but in total objectivity I've read more than 5 books with NowLedge and could not do without it now.
If it's useful for you I'm happy :)
GitNoter
NowLedge
NowLedge