Gyford uses post-it notes inside book covers, rather than the margins, as his note-taking substrate:
When I start a new book I stick a few post-its on the first page inside the cover. That way there's always some paper around to write notes on. [...] when I come to type up the notes (so I never lose them and can search them), the post-its stick handily to the side of the monitor.
See also: discussion on 43Folders
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