Comment prominence determined by value
Milk and Cookies has the best comments of any public viral site. The only reason for this seems to be that interesting users tend to hang out there. It's only a matter of time before spammers and trolls render the comment section futile.
Rather than sequencing comment threads chronologically, they could be sequenced by how much anyone might want to read them. Comments can get up-down thumbs or similar, and the score of the user thumbing the comment should affect the influence of the thumbing. Don't do something stupid, like giving a million-point user four orders of magnitude more influence than a hundred-point user, or a negative-point user negative influence, but do have some decent formula for giving more influence to users who matter.
Unlike YouTube, which has dozens of good comment sprinkled throughout thousands of inane semi-random character sequences, Milk and Cookies could take the revolutionary step of ...drum roll... moving the good comments up and the bad comments down within a given thread terrace. You could even get really fancy, and give the stupid stuff a smaller, paler font so a human can see which comments not to bother reading.
I find it amusing that there's a tight budget on how many videos a user may submit, but there's no limit on how many walls of text can go in the comment section. The pages are reviewed by humans before being allowed an obscure, out-of-the-way place in the database, yet comments just go straight onto the page and stay forever unless an administrator smites a comment on a conduct violation.
So here are my recommendations:
* Up-down thumbs on comments.
* Influential users have bigger thumbs.
* A comment's score is visible somewhere in the corner.
* Good comments move up within their parent thread, bad comments move down.
* Really bad comments get more muted font presentation.
* (extra credit) a user can toggle "sort comments chronologically"
* (extra-extra credit) a user can ask to see a replay of how the comment tree grew.