I have a pretty good method down now that might work for others. Whenever I'm reading a (non-fiction) book I put a dash in the margin next to any important point. I usually have two or three marks per page. Then after I'm done reading I go back and retype the sentences I marked into a MindMap. That way I can read the book at a reasonable speed since I'm not making marginalia, and after I'm done with the book it takes maybe three or four hours to transcribe into the MindMap.
Typing out the full text of the interesting parts of the books is relatively fast since I am a fast typist, only slightly longer than condensing it down into quick notes.
The MindMap itself has a few advantages. First, the hierarchical nature of the software provides built in context and allows me to mentally switch gears between the different layers of the argument very fast. Because of this I often am able to create new ideas that I wouldn't have been able to have otherwise. It also makes it very easy for me to incorporate the important parts of the book into other projects later. If someone says something that reminds me of a book on news.yc, I can find the relevant quote and have it cut-and-pasted into the comment field in less than a minute.
Also, because I organize all my startup ideas and other projects in MindMaps, I can easily drag and drop an entire book directly into that project if it is relevant. Then if I'm talking to someone about the project and they ask me a question, I can look up the answer almost instantly if I don't already know it offhand.
FreeMind is the best product out there because of its speed and its emphasis on folding. The latter part might not make any sense until you play around with it for a while and start making really big maps.
Not that I ever learnt how to do this though, not even after I put a full 15 minutes of effort into it.
Concerning this kind of spead-reading; in my experience it's great for alpha-subjects (is that English? It means non-scientific in Dutch). I used to be able to read 400 page books at 40 (or 60, or 80, probably 80 because my memory is always exaggerated) seconds per page and still get enough out of it to pass the tests.
Comprehension always trumps speed. I'm always surprised by people who say "I've read that book in an hour" or something like that. When I read, I get hundreds of ideas and have hundreds of questions in my head and I usually either write them down or look up the references on the web. That takes time.
I read a lot and the only piece of advice that has worked is: stay focused and concentrate on what you're reading. Don't have an email client open, don't have a dozen tabs open... just eliminate all of the distractions and concentrate on what you're reading.