A clock signal in a computer synchronizes commands by providing a timing reference that coordinates the execution of instructions within the CPU. In Intel processors, this clock signal ensures that data is processed in a systematic manner, allowing for efficient operation. The concept of pipelining refers to the technique where multiple instruction phases are overlapped, improving throughput by allowing the CPU to work on several instructions simultaneously. This means that while one instruction is being executed, another can be decoded, and yet another can be fetched, enhancing overall performance. Understanding these concepts is crucial for grasping how modern CPUs operate efficiently.