I started taking research notes this year in a similar way to the linked article: a document of quotes from books and blogs clipped with my comments. It is sort of magical the result, you reveal big ideas that talk to each other across the divisions of books. You can see it on this site, it really seems the ideas fit together into parts of a coherent overall image.
One difference in my method to Bret's is that I print my notes and put them in a binder. The physical result seems to make the ideas "more real" than when they are buried in text files.
Highly recommend this practice. Everyone has their own big ideas,perhaps only sub consciously voiced and this sort of activity helps bring them to life.
Thanks for the great link!