Directions of software technologies for innovative HPC environments are discussed according to the industrial user requirements for heterogeneous multidisciplinary applications, performance portability, rapid prototyping and software reuse, integration and interoperability of standard tools. The various issues are demonstrated with reference to the PQE2000 project and its programming environment SkIE (Skeleton-based Integrated Environment). Modules developed by a variety of standard languages and tools are encapsulated into SkIECL (SkIE Coordination Language) structures to form the global application. A performance model associated to SkIECL allows the static and dynamic tools to introduce a large amount of global optimizations without the direct intervention of the programmer. The paper discusses also some of the most critical issues in matching architecture and software technology, showing how the SkIE environment, and its evolutions, can act as a solid framework in which innovative hardware-software systems for HPC can be studied and experimented.