I see http://searchyc.com/ mentioned every other day, might be that HNers are overwhelmingly not aware of it, and many don't know how to search just any site with Google. If that's the case then it begs to be linked to from the front page, or a simple search field needs to be put up that will take your query and put it into Google like so:
In the footer the google (site:...) one is there, but no one ever checks the footer and it is just a link.
I think that it was put there after the previous big complaint thread about search but it hasn't helped any and the best way to search is still searchyc.
SearchYC's benefit is not that it gives more current results: it allows you to search comments by, e.g., their author in ways that Google, being a general search engine, cannot.
These days, if all the pages on a site are publicly spidered, then it's likely that Google will do a great job of searching your site for you.
I've seen many sites with terrible search boxes that look like they use the built-in MySQL full-text search. I find I often get better results by just searching through Google with a site: tag.
It makes me think of cases where OpenID is used over in-house authentication. Why maintain something when there are already free systems that will do that for you and have worked out all the kinks?