I sometimes receive comments via email and on this blog along the lines of "What do you think about the criticisms of skeptic X on web site Y?"
The answer is "Not much." In most cases I've found it to be a waste of time to respond to long-winded, free-ranging critiques appearing on blogs and in magazines. Articles published in journals aren't perfect either, but at least they provide a first-pass verification that the critiques seemed reasonable to a few referees. One hopes that the selected referees were knowledgeable about the topic at hand, which is not always the case, but compared to the level of discourse one sees in most op-eds, journal articles are a far superior way to debate controversial topics.
So my response to most web critiques is this: If the author of a detailed critique is confident about their opinion, then they should publish it in a journal. Sometimes when I run across a comment on a web page that is flat wrong, and it's easy to correct, I may comment on it here.