My guide to a good talk page indentation system is based on numbered section style. It might help to think of discussions as a report with numbered sections and subsections where the material is not written in chronological order however when each part is written it still goes in the right place. Each rule is followed by an example: in these examples the bolded line is the most recently added comment, which illustrates the rule it follows. As an aside, discussions should always have a level-2 heading with that oh-so-helpful [Edit] link that comes with section headings. My version of properly is as follows:
1. Comments appear beneath the comment they are a reply to.
2. If two comments exist in reply to one specific comment, they should be at the same level of indentation with the oldest comment at the top (that is, immediately below the comment it is made in reply to).
3. Any reply to a comment should be placed below that comment at the bottom of the list of that comment's replies. If the comment you are replying to is in a list itself, your reply should should appear before the next comment in that list.
4. A comment that is being added to a list of replies should go at the bottom. This includes any sub-threads which follow the last item in that list; do not seperate a comment from its replies.