In this paper, we describe our experience in designing real-time hardware/software systems for data acquisition and analysis applications in particle physics, which are based on a system-on-chip (SoC) approach. Modern field-programmable gate array (FPGA) devices with embedded reduced instruction set computing (RISC) processor cores, high-speed low voltage differential signaling (LVDS) links and ready-to-use multigigabit transceivers allow development of compact systems with a substantial number of input-output (IO) channels, where required performance is obtained by a subtle separation of tasks among closely cooperating programmable hardware logic and user-friendly software environment. We report on the implementation of two such systems to illustrate the advantages of the SoC architectures. One is a flexible test bench for the off-shore read-out system of the ANTARES neutrino experiment. Another is a selective read-out processor device for the CMS electromagnetic calorimeter at LHC.