FPGA devices are often used in High Energy Physics and accelerator technology experiments, where the highest technologies are needed. To make FPGA based systems more flexible, common technique is to provide SoC (System on a Chip) solution in the FPGA, which is in most cases a CPU unit. Such a combination gives possibility to balance between hardware and software implementation of particular task. SoC solution on FPGA can be very flexible, because in simplest cases no additional hardware is needed to run programs on CPU, and when system has such devices like UART, SDRAM memory, mass storage and network interface, it can handle full featured operating system such as Linux or VxWorks. Embedded process can be set up in different configurations, depending on the available resources on board, so every user can adjust system to his own needs. Embedded systems can be also used to perform partial self-reconfiguration of FPGA logic of the chip, on which the system is running. This paper will also present some results on SoC implementations in a Low Level RF system under design for the VUV Free Electron Laser, FLASH, DESY, Hamburg.