I normally keep a pencil with me whenever I am reading something, and will just lightly underline text that I like: phrases, words etc. Then, when I reach a natural conclusion in the book (end of the chapter/section), I'll make a note of it in my pocket-sized journal, which I keep with me at all times. If you can't underline, write it straight into your journal. (I like the previous poster's comment on using an A4 piece of paper in half, that's a nice idea, and I may try that myself).
If something I'm reading triggers any idea at all, I will immediately write it down in my journal once I reach the end of the sentence, typically with the date, book name, and page number (if necessary). I dread the idea of letting ideas go to waste! I find that, once you get used to jotting down brief points quickly, it doesn't stop the enjoyment of the book. If anything, it increases it because I'm free to concentrate on reading instead of letting my mind worry about trying to remember things.
Finally, I recommend writing a review of the book as soon as you're finished, referring to your notes if necessary. Try summarise the book in a few lines, then look at what you liked/disliked both as a reader, and as a writer. Doing it immediately is important, because the things that stayed with you after you finished are, generally speaking, the most important.