I think doing automated queries to search engines is tricky business, and many sites and programs have been either banned or penalized in some way in the past. There may be a good tool, but I think usually such tools are done in a small control group versus publicly available.
(though I may stand corrected by someone who can produce info about a tool)
What I sometimes do is manually is look up the page rank in Google, displaying 100 results per query, then using the browser 'Find' to search for the site. But that's only if it's below 1,000, or 500. I simply don't have the patience to do it any more than that.