The focus of the computer engineering capstone design classes at the University of Alabama in Huntsville, UAH, has been the application of modern design methodology to the development of electronic systems that have both digital hardware and software components. In these classes, it is stressed that efficient digital system design involves the careful consideration of the many possible hardware/software design trade-offs - areas which we feel are the cornerstone of the Computer Engineering discipline. This paper describes the manner in which FPGA-based rapid prototyping techniques have been applied to allow students to empirically explore sets of design alternatives that span the entire hardware/software continuum.