But I think this whole 'bubble popular stuff up' is a tad off. Its too binary, IMO humans aren't all that binary - not all of us anyway. How about you use sliders so people can rate stuff more subjectively and you can also use relative font sizes to size up stuff which is more popular and reduce the font size on stuff that isn't. This does not mean that the text becomes too big or too small - its just a subtle change.
This will allow you to disable this whole bubbling scheme and keep things in a natural chronological order while making it easy to spot popular stuff without adding any cognitive load.
Finally, a discussion board must really have a feature that shows all 'unread' or 'updates since your last post' threads in bold or some sort of highlighting. While news.ycombinator implements the unread piece it would be helpful if it highlighted updated threads also.
How can I be sure you read this comment?