Sophisticated embedded systems are increasingly used in defence, aerospace and avionic industries. They are responsible for control, collision avoidance, pilot assistance, target tracking, navigation and communications, amongst other functions. In this industrial field, High Performance Embedded Computing (HPEC) applications are becoming highly sophisticated and resource consuming for three reasons. First, they should capture and process real-time data from several I/O sources in parallel. Second, they should adapt their functionalities according to the application or environment variations within given Size Weight and Power (SWaP) constraints. Third, since they process several parallel I/O sources, applications are often distributed on multiple computing nodes making them highly parallel. The problem with current HPEC systems is that, they are usually built to meet the needs of a specific application, i.e., lacks flexibility to upgrade the system or reuse existing hardware resources. Due to the hardware parallelism and I/O bandwidth offered by Field Programmable Gate Arrays (FPGAs), application can be duplicated several times to process parallel I/Os, making Single Program Multiple Data (SPMD) the favorite execution model for designers implementing parallel architectures on FPGAs. Furthermore Dynamic Partial Reconfiguration (DPR) feature allows efficient reuse of limited hardware resources, making FPGA a highly attractive solution for such applications. This paper will address HPEC application design challenges and will discuss some solutions relying on FPGA technologies and referring to several industrial collaborations.