TweetMeme, the quickly-growing site that lists the most popular links on Twitter, is launching an overhauled version today that the startup is calling TweetMeme V2. The company says that today’s release includes “a total rewrite” of its scoring system, which will likely affect how quickly and what type of stories appear on the site.

Given that the site isn’t live yet we can’t test the new engine, but TweetMeme says that the new ranking engine will provide “more varied and better quality content”, which will be helped in part by a new kudos scoring system that can change the weight of individual Twitter users. The site is also introducing an improved filtering engine, a new comment system (you’ll now be able to take a comment on the site and retweet it), and a flagging system that lets users bury bad entries. A more robust analytics package will also be appearing next week.

Another interesting note: TweetMeme is teaming with JS-Kit to add support for its real-time commenting engine Echo , which will now be able to import TweetMeme contents into blogs. TweetMeme will also begin promoting Echo, presumably in the hopes of having its reach widened as its comments appear in more blogs.