How should you annotate books? is apparently a lively discussion in some parts of the world.
To extend the rule meme:
Rule 1. Any book with highlighting will make the person who highlit the passages seem insane. Same goes for notes. By symmetry then, our own notes are insane and at best only useful during the reading.
Rule 2. Books take a while to be digested -- e.g. the passages with the most currency will only be revealed well after a book has been laid to rest (i.e. weeks after transcribing the good passages and writing its review), and they won't always be the passages you transcribed.
Rule 3. Invert Rule 1 and find commentary that you enjoy. Try to make your commentaries more like those commentaries.