In the last twenty years, the Internet has grown from a simple, small network to a complex, large-scale system. While it was originally used to offer static content that was organized around simple websites, today, it provides both content and services (e.g. chat, e-mail, web) as well as the outsourcing of computation and applications (e.g. cloud computing). Attackers are not indifferent to this evolution. Often driven by a flourishing underground economy, attackers are constantly looking for vulnerabilities, misconfigurations and novel techniques to access protected and authorized systems, to steal private information, or to deliver malicious content. In this thesis, we advance the state of the art in large scale testing and measurement of Internet threats. We research into three novel classes of security problems that affect Internet systems that experienced a fast surge in popularity (i.e., ClickJacking, HTTP Parameter Pollution, and commercial cloud computing services that allow the outsourcing of server infrastructures). We introduce the first, large scale attempt to estimate the prevalence and relevance of these problems on the Internet.