http://www.nicovideo.jp
I'm surprised nobody thought of this earlier. Also, damn, why didn't I think of that?
Basically, submit a video url from YouTube or Amebavision. You'll then get your own little page where people can then submit comments at any point in the video. This will show up on the right including the time in the video when the comment was made. This will then show up when other people watch the video. You can even format the text a little like position, color, etc.
And of course, if the text is distracting, you can always go to the original source or turn comments off.
This results in something like this: (it's 2 music videos merged together). Most of the comments are people repeating the lyrics.
For something less crazy, try this:
The comments are pretty funny if you can read it. Like when it was showing Cid, someone said "Cid is my bride" and then they comment on the music, or during special scenes like the summons they get all excited.