The present invention describes systems 1, 12 and methods for control of optical devices and communications subsystems. The control system comprises ASIC sub-modules and programmable circuitry 25 which may be integrated into a self-contained, stand-alone module. In one embodiment, the module has one or more FPGAs 25 in conjunction with RF and Digital ASICs 30, an integrated cross-connect 36 between the FPGA and digital and RF ASIC building blocks, and an integrated cross-connect 41 between the ASIC and optical circuits and supporting functions. Programmable chip control and other transmission and tuning functions, programmable transponders, and each FPGA/ASIC 25, 30 that is incorporated into a transponder form factor or a host board, can have the same or different functionalities and other parameters including but not limited to modulation format.