I am working on a web-based documentation tool that is going to have that sort of flowchart style with scrolling. I started work on an Expose-like feature to smoothly scale boxes of information as you moved further out in the tree. So far that part has been a miserable failure.

In my case, there's going to be a lot of cross-linking between documents, so it makes a bit more sense to use that approach. For a comment/conversation type thing, I'm not sure it would be that useful unless you're specifically going to cross-reference conversations.