For most startup founders, launch day is a nerve-wracking blend of excitement and worry. But for Shivaun Raff and her husband, Adam, that day in June 2006 turned into a nightmare they hadn't seen coming.

Their new venture, Foundem—a unique price comparison website they'd left stable careers to create—was finally live. But soon after launch, Foundem practically vanished from Google. Marked as spam by Google's algorithm, the site was buried deep in search results for terms like...