The team behind the Million Short search engine writes,

Million Short is an experimental web search engine (really, more of a discovery engine) that allows you to REMOVE the top million (or top 100k, 10k, 1k, 100) sites from the results set. We thought might be somewhat interesting to see what we'd find if we just removed an entire slice of the web.

One thing to remember that this removes the top overall popular websites from appearing in the results, NOT the top results for a particular search term.