When anybody can publish a URL commenting on another URL, the web is working exactly as it should. The missing piece is a meta-comment system (maybe some microformat) that lets you know when someone else is explicitly commenting on your URL.
Let's say I post a YouTube video (and there is no comment section), and someone else writes about it on their Tumblr using a format using an anchor tag with a rel=comment or something. Then the meta-comment service (where I have registered my YouTube channel and the Tumblr user has registered their blog) notifies me that this person has commented on my video. I could publish a reply on Tumblr to their original Tumblr post, and they would similarly be notified.
A page on the meta-comment service or a little JS widget could even show the comment reply tree across sites.