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Possible Duplicate:
Hierarchical comments usability issues

What are the best options to highlight a reply to a comment ? I'm thinking 3 levels maximum.

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I would have to say that indentation are the best. Is there a reason why you don't want to do indenting?

But if that is not an option I could see borders being used. A thinker right border would cause a slight indentation. the deeper the comment the bigger the right border. See example below.

mockup

download bmml source – Wireframes created with Balsamiq Mockups

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