I run a niche web app that has about 3000 unique visitors a week. People generally agree it's the best resource for its purpose and there was an article in one of the bigger local newspaper about it too. There are no ads or other shadiness on the site. It used to rank between 3 to 5 for the couple of obvious search terms, but since a site overhaul the ranking has tanked. I contacted Google via GWT but no response (though in the past they've been helpful a few times).