What's interesting about online comments is that the comments themselves become a part of the "landscape" of a site. So a site could be aesthetically pleasing and designed well (i.e. no apparent "broken windows" as Kottke would define them), but if the comments are full of expletives and "roflmao" type messages, then they effectively become the broken windows.

If I were to apply the broken windows theory online, I'd consider "bad" comments as graffiti and "good" comments as public art. The broken windows would be more an analogy of a community misusing what's been made available to them as opposed to a designer purposely or accidentally creating something ugly.