I bet there are types of searches for which excluding popular sites works well -- for example, trying to find less popular stuff, which is something that popular websites don't do that good of a job of covering. "Indie" topics, if you will. Would you try to discuss an indie movie on a website chock full of discussions about the latest blockbuster? Then when you search, don't you want to look at less popular movie websites to find the good discussion about your indie movie?
Aw come on, if HN's UI would be "advanced"[0] enough that it would collapse low-scoring comments[1], it would actually make sense to downvote this. But now it just seems petty.
[0] you know, like Reddit.
[1] or if its HTML wouldn't be so horrid to make me give up in despair every time I think to script myself such a thing (as none of the existing 3rd party solutions seem to have gone through the trouble of testing on Opera)