At BarCamp Liverpool I did a session titled "Create a better seach engine than Google" about website search engines covering how search is presented on HE websites and some ways to improve results and user experience.
We've done some nice work on our site search. It no longer searches HTML pages, but the underlying databases, plus pulls out commonly searched terms and has pre-prepared suggestions.
This was based on studying a years worth of search queries.
Try it: http://www.ecs.soton.ac.uk/
It searches our members, research projects, research themes, publications, press releases, and a few other odds and ends.
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