Daniel at "Hack Your Day Productivity" offers a list of interesting tips:
Positioning your metadata – The most important thing when placing your metadata in your Moleskine is to go inwards. Put the most relevant or most important bit of data on the outermost part, since this is easiest to access.
Use information relevant to you – Just because all of us always put in page numbers and titles at the top, this doesn’t mean you have to too. You may have a book of thoughts where page numbers don’t really mean anything.
Using tags and categories – Tags and categories can be used with Moleskine notebooks, not just blogs and web pages. In the same way you categorize a post, you can do so with an entry in your Moleskine.
Further customization – As I just said, the possibilities really are endless. You can cut off the corners of some pages to indicate they are no longer in use, you can cut away corners in different ways to indicate different categories.
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