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YouTube, Google Video, and Grouper brought video-sharing to the 'masses'. They initially dealt with uploading videos and sending video URLs to friends. The next step was associating one video with another (usually via a 'similar videos' list). But now we are getting more sophisticated.
One new website, Motionbox allows users to define and link to a particular portion of a video (via start point and end point). Google Video allows you to link to a particular starting point. And, finally, Grouper is allowing users to leave video comments based on an originating piece of video.
And now it's time for a shameless plug: Several months ago we at MSRA's CID released a technical report about recording audio and video for the purpose of sharing (as in audio/video podcasts). The short paper explains our concept of 'quoting' from media files in order to comment on them or to link to certain sub-segments. Linking to, and commenting on, subsections of time-based media segments is missing from current systems and we felt that doing so should be possible on devices where users consume this type of media: mobile devices. Commenting, in particular, may be most useful when the user can indicate which portion of the media file they are commenting on, rather than the entire segment.
This page has a great example of video commenting - hit the "Menu" button and hit "View All Comments" and then choose the ones you want to see. This works for little funny clips but doesn't let commenters be specific when it comes to longer video segments.