Hermes is a middleware system for design and execution of activity-based applications in distributed environments. It supports mobile computation as an application implementation strategy. While middleware for mobile computing has typically been developed to support physical and logical mobility, Hermes provides an integrated environment where application domain experts can focus on designing activity workflow and ignore the topological structure of the distributed environment. Generating mobile agents from a workflow specification is the responsibility of a context-aware compiler. Hermes is structured as a component-based, agent-oriented system with a 3-layer software architecture. It can be configured for specific application domains by adding domain-specific component libraries. The Hermes middleware layer, compilers, libraries, services and other developed tools together result in a very general programming environment, which has been validated in two quite disparate application domains, one in industrial control and the other in bioinformatics. In the industrial control domain, embedded systems with scarce computational resources control product lines. Mobile agents are used to trace products and support self-healing. In the bionformatics domain, mobile agents are used to support data collection and service discovery, and to simulate biological system through autonomous components interactions.