So the developer of the Retweet iPhone application, Colin Tulloch, decided to take a crack at this problem. The result? An elegant Twitter Web app, ThreadedTweets, that not only organizes @replies, but updates in real-time and seamlessly integrates Twitter Search.
You're given a lot of options when you arrive at ThreadedTweets, even without logging in. The homepage provides a sampling of what this app has to offer, specifically the threaded reply system. Like a message board, individual tweets display how many @replies they elicited. Clicking on this displays the specific replies, which opens up the entire Twitter conversation in an uncluttered fashion. The homepage specifically aggregates some of the top tweets of the day with their @replies.
Is it perfect? No, but it's pretty darn good at finding @replies. Just try clicking "view replies" to see it download the conversation.
Once you've logged into ThreadedTweets via Twitter OAuth (a nice feature), you'll immediately notice that ThreadedTweets updates tweets in real-time. In that regard, it's a lot like Twitzap. ThreadedTweets, however, has a slider that helps you control the speed at which you want updates. If you want to stop all updates, just slide ThreadedTweets all the way to the right. One more cool thing: ThreadedTweets even has its own Real-time widget.