Web-based applications and services are increasingly being used in security-sensitive tasks. Current security protocols rely on two crucial assumptions to protect the confidentiality and integrity of information: First, they assume that end-point software used to handle security-sensitive information is free from vulnerabilities. Secondly, these protocols assume point-to-point communication between a client and a service provider. However, these assumptions do not hold true with large and complex vulnerable end point software such as the Internet browser or web services middleware or in web service compositions where there can be multiple value-adding service providers interposed between a client and the original service provider. To address the problem of large and complex end-point software, we present the AppCore approach which uses manual analysis of information flow, as opposed to purely automated approaches, to split existing software into two parts: a simplified trusted part that handles security-sensitive information and a legacy, untrusted part that handles non-sensitive information without access to sensitive information. Not only does this approach avoid many common and well-known vulnerabilities in the legacy software that compromised sensitive information, it also greatly reduces the size and complexity of the trusted code, thereby making exhaustive testing or formal analysis more feasible. We demonstrate the feasibility of the AppCore approach by constructing AppCores for two real-world applications: a client-side AppCore for https-based applications and an AppCore for web service platforms. Our evaluation shows that security improvements and complexity reductions (over a factor of five) can be attained with minimal modifications to existing software (a few tens of lines of code, and proxy settings of a browser) and an acceptable performance overhead (a few percent). To protect the communication of sensitive information between the clients and service providers in web service compositions, we present an end-to-end security framework called WS-FESec that provides end-to-end security properties even in the presence of misbehaving intermediate services. We show that WS-FESec is flexible enough to support the lattice model of secure information flow and it guarantees precise security properties for each component service at a modest cost of a few milliseconds per signature or encrypted field.