This is probably going to start a big argument, but what’s the best free search engine available that can be embedded into a website? This is for a non-profit, if that broadens the search any.
You could just use this websearch jQuery plugin I wrote and add any number of search engines to your site. If you want the searches to specifically target your site, you can modify the search string in the plugin to include the site url: “site:http://mysite.com“
There are actually two versions, one is a jQuery UI widget and the other one is independent of jQuery UI.