I like to use Goodreader in my iPad. It let's me create a generated "mini-book" containing all the notes and underlined text with references to the pages containing it.
I'm not that smart so I go through tech books slowly so I can hopefully retain more of it and maybe even apply the knowledge day to day as I acquire it. I've always been jealous of people who rip through a dense (knowledge dense, not pages dense) tech book in a weekend and say they got it all.
The books that are more code oriented, I read on the computer so that I can type and run the code as I work through the book.
The books that are more theory or higher level I read on an e-reader.
In my experience each chapter takes about 2 hours to read and digest. Then I need an hour to summarise and reflect. Followed by another 3-4 hours of practice. By this point I can honestly say I understand and can use the material.
So 6-7 hours per chapter. Most books I read have around 12 chapters and so take a good 72+ hours to read a book. Due to work and family commitments I can only read 3-4 tech books like this per year so I try and pick only the best works.
The value you can get out of this way of reading is phenomenal.
Since you've been so selective with books, what do you recommend?