Today's microprocessors are much more remarkable in their similarities than in their differences, this is not likely to change for the foreseeable future. By combining a fixed set of datapath components with FPGA-implemented interconnect and control, complex systems can be constructed that emulate different microprocessor architectures. This research attempts to identify target applications for which special-purpose processors can offer performance gains. Current areas of investigation include gene sequence analysis and multimedia systems. The objectives of this research are the completion of a quantitative study of the utility of FPGAs in the prototyping of large heterogeneous digital systems, and the development of new FPGA architectures based on this study. The methods employed consist of: (1) the implementation of custom microprocessors and general emulation systems on FPGAs; (2) quantitative analysis of these designs; (3) measurement of performance, power consumption, and other relevant parameters of these designs; and (4) use of results to develop new FPGA architectures better suited to the prototyping of complex digital systems.