Web services standards were designed to enable interoperability of heterogeneous application servers in the Service Oriented Architecture. Although the standards proved to be highly successful, there are still difficulties in effective services integration. The paper presents a methodology that enables description of application servers interoperability in order to improve the service integration process. The methodology proposes a systematic classification of Web services standards, versions and configuration options, and uses the classification for interoperability rating. Concrete integrations are rated by developers that specify integration scope, configuration complexity and required expertise level. The methodology was implemented in a web system that enables definition of standards and configuration options as well as rating of integrations. As a part of the research, interoperability experiments were executed and registered in the system.