The majority of Youtube comments are garbage, so we built Deebrief to allow for insightful comments and interesting questions at particular times in a video. For a good example, see <a href="http://www.deebrief.com/#!/consume/53a37a3ba109a8020091e663" rel="nofollow">http://www.deebrief.com/#!/consume/53a37a3ba109a8020091e663</a>
Really good, to be honest I really don't see me using a separate website to comment on youtube videos, would be a good product to be brought by Google and integrate natively though.