I agree that a “threaded” or otherwise centralized view of the flow of conversation would be incredible. But I don’t want to shut out non-trackback using tools. The referrer is common across all web-platforms — it’s just links, after all!
That being said, for tools that don’t do trackback, you can use Simpletracks from Kalsey Consulting. I use it on occasion, but other times I’ll just do this — post comments on my site as well as type them into the comment box.
Some other thoughts: Is “trackback” capitalized or not? Is it a trademark of MovableType?