My favorite way to increase comprehension is to underline good parts. Once I've read a few chapters, I'll copy the underlined bits out and add in why they caught my eye, whether surprising, beautiful, powerful, or by generating good ideas. At the end of the book, I've got a page or two of quotes and leads to follow. I then score each book 1-10.

I made a small shelf with just the 9s and 10s which are seen on a daily basis. This the good stuff, the top shelf, the cream of the crop. It's great having them close at hand for an additional reading.