I have a few more suggestions, all of which work better if each post has (or at least, can have) a headline (= title = subject).
Suggestion 1: Allow users to explicitly start a new sub-thread within a thread. (Typically, the headline would change for a new sub-thread and it would remain the same if a response were not starting a new sub-thread.)
Suggestion 2: Show a Table of Contents for all the threads and sub-threads in a conversation, at the top of the conversation. The entries in the Table of Contents should all be links that take you to the first post in that thread or sub-thread.
Suggestion 3: Right now you allow users to opt out of updates to specific conversations or opt out of updates to all Civic Commons conversations. It would be desirable to have much finer granularity and allow users to opt in to or opt out of specific threads or specific sub-threads within specific conversations. There should be an option to opt in to or out of "all new threads within a (specific) conversation or all new sub-threads within a (specific) thread or (specific) sub-thread.
As Nancy Reeves points out above, "the tiered (indented) structure stops 3 steps in (after that everything aligns to the same left edge)."
Suggestion 4: Don't fix the width of the window and stop at three levels, keep indenting to an arbitrary depth and keep making the window wider as required (and let users use the horizontal scroll bar in their browsers).
Suggestion 5: Don't indent more for every response to a response to a response. Only increase the indentation when a user declares that he is starting a new sub-thread.
Suggestion 6: Don't be as generous as you currently are with the amount of horizontal space you use for each indentation. If you tighten things up a bit, you'll have room for more levels of indentation in the same amount of horizontal space.
Suggestion 7: (This is a repeat of a suggestion that I made elsewhere in this conversation). Draw lines to indicate how things are connected to each other. All posts linked to the same vertical line would be part of the same thread or sub-thread. A horizontal line would link to the first post in a new sub-thread. (This is probably easier to understand by seeing an illustration than by reading a description.)
Suggestion 8. A Conversation with threads, sub-threads, sub-sub-threads, really becomes an outline structure. Rather than trying to reinvent too much, take advantage of all the work that has already been done with outline software. For example, see the documentation at http://smallpicture.com/fargoPress.html, http://smallpicture.com/fargoDocs.html, and http://smallpicture.com/outlinerHowto.html. Then play with Fargo yourself at http://fargo.io/. (Whether you look at Fargo or not, Nancy Reeves might like taking it for a test drive.)