My problem is that I read a LOT of articles and publications. If I started highlighting things in articles, I would never have enough time to go back to them. Besides, why would I want to? I already read it, which means that it's already in my mind! What's the point of reading stuff if not to put information inside your mind? I'd rather use my time to read more new stuff than to revisit things I already know.
Maybe the solution is not more tools, it's just to stick to topics that interest you and to pay attention and put more thought into what you're reading.
I apologize, I projected my own experience and assumed that other people were able to remember the main points of what they read. I guess most people don't have have great memory. I never thought of myself has having good memory but I remember the main points of most of what I read.