What I would like would be to have a tagging system on comment threads, so that I could filter out comment threads with rough edges if I didn't like them, or threads with endless back and forth nitpicking, or threads that have been covered endlessly before. Something like the old slashdot "Informative" or "Funny" system. Then the ones that wanted could troll and flame away to their hearts content, without disrupting the general discussion of a topic. The "no censorship" crows could turn off filtering alltogether and get HN exactly as it is today.
I think a tagging system is a fantastic idea, especially if users can assign different weights to different tags for sorting and filtering purposes. I haven't seen a discussion system, apart from Slashdot's very limited implementation, that allows comment tagging, and a broader implementation might be wildly successful. You could have a voting mechanic that assigns a score to the comment, then allow users to assign different coefficient values to each qualitative modifier to build their own view. No need to limit it to a small set of predefined tags, either; users could define their own tags a la Delicious.