The JTAG port on Intel processors enable several test and validation functions. These include: "Probe mode", access to the "Control Register Access Bus", execution tracing, performance monitoring and blowing/reading fuses.
Intel uses these modes to bring chips to life. The JTAG TAP port is one of the first components that must be flexed in order to test new chip designs. Motherboard manufacturers rely on these functions to test and validate their bios and products.